tag:blogger.com,1999:blog-75877961492810435892024-03-05T22:30:43.459-08:00All about BioinformaticsAnonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-7587796149281043589.post-61377187995520544362018-03-18T08:13:00.004-07:002018-03-18T08:13:46.901-07:00Facts about Proteins !!!<div dir="ltr" style="text-align: left;" trbidi="on">
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-58230208272636457992018-03-18T08:07:00.000-07:002018-03-18T08:07:49.957-07:00Bioinformatics Memes<div dir="ltr" style="text-align: left;" trbidi="on">
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-38492020878247406342017-09-24T05:43:00.000-07:002017-09-24T05:58:47.699-07:00Bioinformatics scholarship 2017<div dir="ltr" style="text-align: left;" trbidi="on">
I am posting some useful links to get PhD and masters positions in world,s best universities.The complete list is given below.<br />
<h4 style="text-align: left;">
<span style="color: orange;">1. Beijing Normal University</span></h4>
<b><span style="color: purple;">complete link :</span></b><br />
<a href="http://www.cucas.edu.cn/china_scholarships/detail?id=198&c_id=4234">http://www.cucas.edu.cn/china_scholarships/detail?id=198&c_id=4234</a><br />
<br />
<h4 style="text-align: left;">
<span style="color: #3d85c6;">2.ETH Zurich</span></h4>
<span style="color: purple;"><b>complete link:</b></span><br />
<a href="https://www.ethz.ch/en/studies/prospective-masters-degree-students/masters-degree-programmes/engineering-sciences/master-computational-biology-and-bioinformatics.html">https://www.ethz.ch/en/studies/prospective-masters-degree-students/masters-degree-programmes/engineering-sciences/master-computational-biology-and-bioinformatics.html</a><br />
<br />
<h4 style="text-align: left;">
<span style="color: #990000;">3.Other universities bioinformatics programs</span></h4>
<div>
<b><span style="color: purple;">complete link:</span></b></div>
<a href="https://www.findaphd.com/search/phd.aspx?SAID=502">https://www.findaphd.com/search/phd.aspx?SAID=502</a><br />
<br />
<a href="https://www.postgraduatestudentships.co.uk/subject/all-subjects/biological-and-life-sciences/bioinformatics/pgr">https://www.postgraduatestudentships.co.uk/subject/all-subjects/biological-and-life-sciences/bioinformatics/pgr</a><br />
<br />
<a href="https://www.phdportal.com/studies/63735/bioinformatics.html">https://www.phdportal.com/studies/63735/bioinformatics.html</a><br />
<br />
<h4 style="text-align: left;">
<span style="color: #6aa84f;">4. LUND university</span></h4>
<div>
<b><span style="color: purple;">complete link:</span></b></div>
<div>
<span style="color: blue;"><a href="http://www.lunduniversity.lu.se/lubas/i-uoh-lu-NABIF/18010">http://www.lunduniversity.lu.se/lubas/i-uoh-lu-NABIF/18010</a></span></div>
<div>
<br /></div>
<div>
<br /></div>
<h4 style="text-align: left;">
<span style="color: #a64d79;">5. Cranfield university</span></h4>
<div>
<b><span style="color: purple;">complete link:</span></b></div>
<div>
<b><span style="color: purple;"><a href="https://www.cranfield.ac.uk/courses/taught/applied-bioinformatics">https://www.cranfield.ac.uk/courses/taught/applied-bioinformatics</a></span></b></div>
<div>
<b><span style="color: purple;"><br /></span></b></div>
<br />
<br />
<br />
<br /></div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-49704336368505486422017-08-17T11:11:00.000-07:002017-09-24T03:39:48.168-07:00Variant discovery and analysis pipeline for whole genome/exome/targeted genome sequencing<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="background-color: white; color: #333333;"><span style="font-family: "verdana" , sans-serif;">SNPs (Single Nucleotide Polymorphisms) are genetic markers of choice for both linkage and association mapping and for population structure and evolution analysis. They are virtually unlimited, evenly distributed along the genome, bi-allelic and co-dominant.</span></span><br />
<span style="font-family: "verdana" , sans-serif;"><b style="background-color: white; color: #222222;">Single nucleotide polymorphism (SNP</b><span style="background-color: white; color: #222222;">) </span><b style="background-color: white; color: #222222;">detection</b><span style="background-color: white; color: #222222;"> technologies are used to scan for new polymorphisms and to determine the allele(s) of a known polymorphism in target sequences.Identification of SNPs is helpful in identifying the actual cause of genetic diseases..Basic pipeline for identification of SNPs is given below and I hope it will help you in your projects and assignments.</span></span><br />
<span style="font-family: "verdana" , sans-serif;"><span style="background-color: white; color: #222222;"><br /></span></span>
<br />
<div class="MsoListParagraphCxSpFirst" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">1)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">To convert SRA file
downloaded from NCBI into fastQ format<o:p></o:p></span></u></b></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">fastq-dump.2.3.5
--origfmt --split-3 SRR1915421.sra</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">where<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l4 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">fastq-dump.2.3.5 is the command to convert
sra into fastq<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l4 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">SRR1915421.sra is file downloaded from NCBI
SRA<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">2)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Making index files of
reference sequence<o:p></o:p></span></u></b></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">bwa
index -a bwtsw -p hg19.fa</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l0 level1 lfo3; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">where hg19.fa is the human reference sequence
downloaded from UCSC browser<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l0 level1 lfo3; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">bwa index command is used to make indexes of
reference<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<div class="MsoListParagraphCxSpLast" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">3)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Alignment is done using BWA
aligner<o:p></o:p></span></u></b></div>
<div class="MsoNormal" style="margin-left: .25in;">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">bwa
aln -t 30 -f SRR.sai ../../indexes/hg19/hg19 SRR1915421.fastq</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpFirst">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">where<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l7 level1 lfo4; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">bwa aln is command to align the reas on
reference genome<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l7 level1 lfo4; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">SRR.sai is the name of file that will be
obtained as a result of alignment<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l7 level1 lfo4; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">SRR1915421.fastq is the file that is to be
aligned on reference genome<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">4)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Formation of SAM file<o:p></o:p></span></u></b></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">samse
-f ERR.sam -r
'@RG\tID:D3NH4HQ1\tPL:illumina\tPU:D3NH4HQ1:139:C153UACXX\tLB:6\tSM:SRR1915421\tCN=nad'
../../indexes/hg19/hg19 SRR.sai SRR1915421.fastq</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">where<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l6 level1 lfo5; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">samse is used when we have single end data
sampe is used when paired end data<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l6 level1 lfo5; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">ERR.sam is the name of sam file that will be
generated using the above mentioned command<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l6 level1 lfo5; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">'@RG\tID:D3NH4HQ1\tPL:illumina\tPU:D3NH4HQ1:139:C153UACXX\tLB:6\tSM:SRR1915421\tCN=nad'
is the format of the NGS read file<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l6 level1 lfo5; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">SRR.sai is the file obtained as a result of
alignment<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l6 level1 lfo5; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">SRR1915421.fastq is the read data<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">5)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Validation of SAM file and SAM to BAM
conversion<o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">java -jar picard.jar ValidateSamFile
I=ERR.sam MODE=SUMMARY</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpLast" style="margin-left: 106.5pt; mso-add-space: auto; mso-list: l8 level1 lfo6; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 14.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">where I =
input and ERR.sam is the sam file</span><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-left: 88.5pt;">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><span style="color: orange;">java -Xmx4g -Djava.io.tmpdir=/tmp -jar
../../../softwares/picard-
tools-2.1.1/picard.jar SortSam SO=coordinate INPUT=ERR.sam
OUTPUT=SRR.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true</span><o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-left: 88.5pt;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">where<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpFirst" style="margin-left: 106.5pt; mso-add-space: auto; mso-list: l8 level1 lfo6; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">CREATE_INDEX argument to true we automatically create an
index file for the generated bam file.<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 106.5pt; mso-add-space: auto; mso-list: l8 level1 lfo6; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">SRR.bam is the bam file obtained as a result of conversion of
sam<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 106.5pt; mso-add-space: auto; mso-list: l8 level1 lfo6; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt; line-height: 107%;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">By setting the validation stringency to lenient, picard
ignores some validation errors which frequently occur at the alignment step.</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;"><o:p></o:p></span></div>
<div class="MsoListParagraphCxSpLast" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">6)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Marking
duplicates<o:p></o:p></span></u></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"> <span style="color: orange;"> java -Xmx4g
-Djava.io.tmpdir=/tmp -jar ../../../softwares/picard- tools-
2.1.1/picard.jar MarkDuplicates INPUT=SRR.bam OUTPUT=SRR.marked.bam
METRICS_FILE=metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT</span><o:p></o:p></span></b></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">where<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l3 level1 lfo7; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">SRR.marked.bam is the file that contains
the duplicates<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l3 level1 lfo7; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">Again the validation
stringency is set to lenient but no index is created as we will perform more
changes on the output bam file.</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">7)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;">
</span></span></b><!--[endif]--><b><u><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt;">Local realignment around indels</span></u></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">Indels within reads often lead to false positive SNPs at the
end of sequence reads. To prevent this artifact, local realignment around
indels is done<span class="apple-converted-space">. It is done in two steps<o:p></o:p></span></span></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"><span style="color: orange;">java -Xmx4g -jar ../../../softwares/GenomeAnalysisTK.jar -T
RealignerTargetCreator -R ../../indexes/hg19/hg19.fa -o SRR.bam.list -I
SRR.marked.bam</span><o:p></o:p></span></b></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">This step creates the file in the form of
table format which is SRR.bam.list<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Where<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l1 level1 lfo8; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">SRR.bam.list is the file in table format
that can be used further for realigning step<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l1 level1 lfo8; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">SRR.marked.bam is the marked duplicate file
obtained in the previous step<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<br /></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">2<sup>nd</sup> step<o:p></o:p></span></b></div>
<div class="MsoPlainText">
<br /></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"><span style="color: orange;">java -Xmx4g -Djava.io.tmpdir=/tmp -jar
../../../softwares/GenomeAnalysisTK.jar -I SRR.marked.bam -R
../../indexes/hg19/hg19.fa -T IndelRealigner -targetIntervals SRR.bam.list -o
SRR.marked.realigned.bam</span><o:p></o:p></span></b></div>
<div class="MsoPlainText">
<br /></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">This step will generate
SRR.marked.realigned.bam file<o:p></o:p></span></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">While working on paired end data<o:p></o:p></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">Java -Djava.io.tmpdir=/tmp/flx-auswerter\ -jar
picard/FixMateInformation.jar \<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">INPUT=input_bam.marked.realigned.bam \<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">OUTPUT=input_bam.marked.realigned.fixed.bam \<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">SO=coordinate \<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">VALIDATION_STRINGRNCY=LENIENT \<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><span style="color: orange;">CREATE_INDEX=true</span><o:p></o:p></span></b></div>
<div class="MsoPlainText">
<br /></div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">8)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Quality
score recalibration<o:p></o:p></span></u></b></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">Quality data generated from the sequencer isn't always very
accurate and for obtaining good SNP calls (which rely on base quality scores),
recalibration of these scores is necessary and is performed in two steps<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="color: orange;"><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;">Java -Xmx4g -jar GenomeAnalysisTK.jar \ </span></b><b><span style="font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">-l
INFO \ -R chr15.fa \ --DBSNP dbsnp132.txt \ -I input.marked.realigned.fixed.bam
\ -T CountCovariates \ -cov ReadGroupCovariate \ -cov CycleCovariate \ -cov
DinucCovariate \ -recalFile input.recal_data.csv</span></b></span><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">This step creates a .csv file which is needed for the next
step and requires a dbSNP file, which can be downloaded at the UCSC Genome
browser homepage<b>(</b></span><a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/"><b><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/</span></b></a><b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;">).</span></b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;"><o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt; line-height: 107%;">Download the dbsnp132.txt.gz file and unzip it using gunzip<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;"><span style="color: orange;">gunzip dbsnp132.txt.gz</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<div class="MsoListParagraphCxSpMiddle">
<b><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">2<sup>nd</sup> step<o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle">
<span style="color: orange;"><b><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">Java -Xmx4g -jar
GenomeAnalysisTK.jar \ </span></b><b><span style="font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">-l
INFO \ -R chr15.fa \ -I input.marked.realigned.fixed.bam \ -T
TableRecalibration \ --out input.marked.realigned.fixed.recal.bam \ -recalFile
input.recal_data.csv</span></b><b><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;"><o:p></o:p></span></b></span></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<div class="MsoListParagraphCxSpLast" style="mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">9)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt; line-height: 107%;">SNP calling<o:p></o:p></span></u></b></div>
<div class="MsoPlainText" style="margin-left: .25in;">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"><span style="color: orange;">java -Xmx4g -jar ../../../softwares/GenomeAnalysisTK.jar
-glm BOTH -R ../../indexes/hg19/chr15.fa -T UnifiedGenotyper -I
SRR.marked.realigned.bam -D ../bwa/snp144.vcf -o SRR.vcf -metrics snps.metrics
-stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A Coverage -A AlleleBalance
-L target_intervals.bed</span><o:p></o:p></span></b></div>
<div class="MsoPlainText" style="margin-left: .25in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">where<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">The “glm both”
argument enables SNP and Indel calling.</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">chr15.fa is the reference genome file<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">SRR.marked.realigned.bam is the realigned
bam file obtained in previous steps<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">snp144.vcf is the raw snp file obtained as
a result of the above mentioned command<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">The metrics file (</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">snps.metrics ) </span><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">specified
by the metrics command contains statistics for the SNP calling step<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .75in; mso-list: l2 level1 lfo9; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12.0pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">The -L command
contains a list of the targeted intervals we wanted to sequence. </span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">To get a bed file for specific gene locus:<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">http://genome.ucsc.edu/cgi-bin/hgTables<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">While downloading. bed
file <span class="apple-converted-space">Choose</span> the hg19 assembly of the
human genome and set the track to RefSeq genes and the table to refGene. Use
BED format as output format and assign the file an appropriate name (I use
target_intervals.bed).<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">10)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;"> </span></span></b><!--[endif]--><b><u><span style="background: white; font-family: "calibri" , sans-serif; font-size: 14pt;">SNP filtering</span></u></b><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"><o:p></o:p></span></u></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">Convert the VCF (variant call format file) into excel format
by just opening vcf file and copy it into excel sheets.<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">Apply filters on specific columns by selecting filter option
in the excel sheets.<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">Some of the filters are<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: 1.0in; mso-list: l9 level1 lfo10; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">QUAL<30 </span><span style="background: white; font-family: "wingdings"; font-size: 12pt;">à</span><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;"> REMOVE THESE SNPs<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: 1.0in; mso-list: l9 level1 lfo10; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">AF>1 </span><span style="background: white; font-family: "wingdings"; font-size: 12pt;">à</span><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;"> remove these as well as frequency greater
than 1 are not SNPs they are known as polymorphisms<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: 1.0in; mso-list: l9 level1 lfo10; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "symbol"; font-size: 12pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">QD (Quality by depth)
<6 </span><span style="background: white; font-family: "wingdings"; font-size: 12pt;">à</span><span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;"> remove these as well<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="background: white; font-family: "calibri" , sans-serif; font-size: 12pt;">To apply more filters
to remove false positive results check the link given below.<o:p></o:p></span></div>
<div class="MsoPlainText">
<b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;"><span style="color: orange;">http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set<o:p></o:p></span></span></b></div>
<div class="MsoPlainText">
<br /></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">11)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;">
</span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">Annotation using SNPnexus<o:p></o:p></span></u></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">In order
to perform functional annotation of SNPs go to the link <b>http://snp-nexus.org/<o:p></o:p></b></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">The SNPnexus is useful for the functional
annotation of SNPs and predicts whether the SNP is damaging or tolerating. For
this purpose, it gives polyphen as well as SIFT scores. Apart from these scores
this online webserver predicts the change in amino acids at specific positions,
disease linked with the snp and predicts whether it is known or Novel snp.<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">To do the annotation simply input the SNP
details manually<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Chromosome 1 190641277 A G 1<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Chromosome 1 190641388 A C 1<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Chromosome 1 190641422 A C 1<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">This format is the easiest way to do
annotation. Many other formats are also available but this is the simple one.<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Chromosome 1 </span><span style="font-family: "wingdings"; font-size: 12.0pt;">à</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"> chromosome number<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">1980875 </span><span style="font-family: "wingdings"; font-size: 12.0pt;">à</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"> chr position<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">A </span><span style="font-family: "wingdings"; font-size: 12.0pt;">à</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"> Ref allele<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">G </span><span style="font-family: "wingdings"; font-size: 12.0pt;">à</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">ALT allele<o:p></o:p></span></div>
<div class="MsoPlainText">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">1 </span><span style="font-family: "wingdings"; font-size: 12.0pt;">à</span><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"> chr band<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in; mso-list: l5 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">12)<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;">
</span></span></b><!--[endif]--><b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt;">Further validation of annotated SNPs<o:p></o:p></span></u></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">To
validate further the annotated SNPs PROVEAN webserver is used. It gives SIFT as
well as PROVEAN scores. These scores predict that whether these SNPs are
damaging, tolerating or benign. If the score is less than 0.05 in case of SIFT
the SNPs are damaging. In case of PROVEAN if cutoff value is below -2.5 then
the SNPs are declared damaging.<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">On the
basis of these Scores get the appropriate SNPs that are damaging and linked
with the disease onset.<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Here is
the link for PROVEAN<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<a href="http://provean.jcvi.org/genome_submit_2.php"><b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">http://provean.jcvi.org/genome_submit_2.php</span></b></a><b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;"><o:p></o:p></span></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<b><span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">format for input:<o:p></o:p></span></b></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">2,230633386,G,C<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">1,100382265,C,A<o:p></o:p></span></div>
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">This is
the simplest format and at a time you can upload number of SNPs.<o:p></o:p></span></div>
<br />
<div class="MsoPlainText" style="margin-left: .5in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt;">Here 2 is
the chromosome number, 234566 is the position of SNP G is the reference allele
and C is the alt allele.<o:p></o:p></span></div>
<span style="font-family: "verdana" , sans-serif;"><span style="background-color: white; color: #222222;"><br /></span></span>
<br />
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<br /></div>
<div class="MsoListParagraphCxSpLast" style="margin-left: 1in; text-align: justify; text-indent: -0.25in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;"><br /></span></div>
<div class="MsoListParagraphCxSpLast" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "calibri" , sans-serif; font-size: 12.0pt; line-height: 107%;"><br /></span></div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><br /></span></u></b></div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><br /></span></u></b></div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<b><u><span style="font-family: "calibri" , sans-serif; font-size: 14.0pt; line-height: 107%;"><br /></span></u></b></div>
<br />
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-85037452492811037952017-04-25T23:54:00.004-07:002017-09-24T03:42:07.406-07:00List of parameters present in Bowtie and BWA aligners<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="font-family: "verdana" , sans-serif;">Here is a complete list of some important parameters used in both aligners to control the alignment of FastQ data.</span><br />
<span style="font-family: "verdana" , sans-serif;"><br /></span>
<br />
<table border="1" cellpadding="0" cellspacing="0" class="MsoTableGrid" style="border-collapse: collapse; border: none; mso-border-alt: solid windowtext .5pt; mso-padding-alt: 0in 5.4pt 0in 5.4pt; mso-yfti-tbllook: 1184;">
<tbody>
<tr style="height: 21.45pt; mso-yfti-firstrow: yes; mso-yfti-irow: 0;">
<td style="border-right: none; border: solid windowtext 1.0pt; height: 21.45pt; mso-border-bottom-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: purple; font-family: "verdana" , sans-serif;">BWA<o:p></o:p></span></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 21.45pt; mso-border-bottom-alt: solid windowtext .5pt; mso-border-right-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: none; border-top: solid windowtext 1.0pt; height: 21.45pt; mso-border-bottom-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: purple; font-family: "verdana" , sans-serif;">Bowtie<o:p></o:p></span></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 21.45pt; mso-border-bottom-alt: solid windowtext .5pt; mso-border-right-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<br /></div>
</td>
</tr>
<tr style="height: 21.45pt; mso-yfti-irow: 1;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 21.45pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: #351c75; font-family: "verdana" , sans-serif;">Parameter<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 21.45pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: #351c75; font-family: "verdana" , sans-serif;">Description<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 21.45pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: #351c75; font-family: "verdana" , sans-serif;">Parameter<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 21.45pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="font-family: "verdana" , sans-serif;"><span style="color: #351c75;">Description</span><o:p></o:p></span></span></b></div>
</td>
</tr>
<tr style="height: 20.35pt; mso-yfti-irow: 2;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Bwa
alignment options<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">There are different parameters for
alignment which are listed below<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-u
20<o:p></o:p></span></span></b></div>
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<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">This option causes Bowtie to exit
after processing first 20 reads from file<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 20.35pt; mso-yfti-irow: 3;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-n NUM</span></b><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Maximum edit distance if the value is INT, or
the fraction of missing alignments given 2% uniform base error rate if FLOAT</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-S<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.35pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">To obtain alignment in SAM format<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 4;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-o</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Maximum number of gap opens</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-l<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">To confirm that output files are
created<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 5;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-e</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Maximum number of gap extensions</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">--suppress<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Suppresses all outputs if columns
number is not mentioned otherwise suppresses the mentioned columns<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 6;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-a</span></b><span style="font-size: 12.0pt;"> STR<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Algorithm for constructing BWT index<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-a<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Instructs bowtie to report all valid alignments
subject to the alignment policy<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 7;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-d</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Consolas;"><span style="font-family: "verdana" , sans-serif;"><br />
Disallow a long deletion within INT bp towards the 3’-end<span class="apple-converted-space"> </span><o:p></o:p></span></span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-k<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Reports all the valid alignments<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 8;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-i</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Disallow an indel within INT bp towards the
ends</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">--best<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Guarantees that bowtie will find and
print the alignments for a given read in best-to-worst order<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 9;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-p</span></b><span style="font-size: 12.0pt;"> STR<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Prefix of the output database<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-p<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Value greater than 1 allows bowtie to
use more than computer processor<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 10;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-l</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Take the first INT subsequence as seed. If INT
is larger than the query sequence, seeding will be disabled.</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">--offrate<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Adjusts the error message about memory
having been exhausted<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 11;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-k</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Maximum edit distance in the seed</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-C<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Enables alignment of color space reads
produced by ABI SOLiD<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 12;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-t</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Number of threads (multi-threading mode)</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-v</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Only alignment up to <int>
mismatches in the entire alignment are considered “valid”<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 13;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-O</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Gap open penalty</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-n</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Only alignment with up to <int>
mismatches in the seed portion of alignment are considered “valid”<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 14;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="background: white; font-size: 12pt;"><span style="font-family: "verdana" , sans-serif;">-I<o:p></o:p></span></span></b></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">The input is in the Illumina 1.3+ read format
(quality equals ASCII-64)</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-l</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">When -n is specified, -l sets the
length of the seed portion of the alignment to <int><o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 15;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-E</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT<o:p></o:p></span></i></span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Gap extension penalty</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-e</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">When -n is specified, -e sets the
limit<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 16;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-b</span></b><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Specify the input read sequence file is the BAM
format. For paired-end data, two ends in a pair must be grouped together and
options<span class="apple-converted-space"> </span><b>-1</b><span class="apple-converted-space"> </span>or<span class="apple-converted-space"> </span><b>-2</b><span class="apple-converted-space"> </span>are usually applied to specify which
end should be mapped.</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-m</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">If bowtie finds more than <int>
valid arguments for a read, suppress all alignments for a read<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 17;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">-M</span></b><span class="apple-converted-space"><i><span style="background: white; font-size: 12pt;"> </span></i></span><i><span style="background: white; font-size: 12pt;">INT</span></i><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Mismatch penalty. BWA will not search for
suboptimal hits with a score lower than (bestScore-misMsc)</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">-M</span></b><span style="font-size: 12.0pt;"> <int><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">If bowtie finds more than <int>
valid alignments for a read, suppress the alignments but report one of them
at random<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 18;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">samse</span></b><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Generate alignments in the SAM format given
single-end reads. Repetitive hits will be randomly chosen.</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><a href="http://bowtie-bio.sourceforge.net/manual.shtml#command-line"><code><b><span style="background: white; color: windowtext; font-size: 12pt; text-decoration-line: none;">-1</span></b></code></a><span class="apple-converted-space"><b><span style="background: white; font-size: 12.0pt;"> </span></b></span><b><span style="font-size: 12.0pt;"><o:p></o:p></span></b></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-1 is specified for single end
alignment<o:p></o:p></span></span></div>
</td>
</tr>
<tr style="height: 19.2pt; mso-yfti-irow: 19; mso-yfti-lastrow: yes;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="background: white; font-size: 12pt;">sampe</span></b><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; font-size: 12pt;">Generate alignments in the SAM format given
paired-end reads. Repetitive read pairs will be placed randomly.</span><span style="font-size: 12.0pt;"><o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.65pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<b><span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">-2<o:p></o:p></span></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 19.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.7pt;" valign="top" width="156"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Specified for paired end alignment<o:p></o:p></span></span></div>
</td>
</tr>
</tbody></table>
</div>
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179472 72.770422600000018 33.9408292 73.415869600000008tag:blogger.com,1999:blog-7587796149281043589.post-73486923357861181152017-04-25T23:49:00.002-07:002017-04-25T23:52:14.036-07:00 General differences between BWA and Bowtie Aligners (NGS data alignment tools)<div dir="ltr" style="text-align: left;" trbidi="on">
<table border="1" cellpadding="0" cellspacing="0" class="MsoTableGrid" style="border-collapse: collapse; border: none; mso-border-alt: solid windowtext .5pt; mso-padding-alt: 0in 5.4pt 0in 5.4pt; mso-yfti-tbllook: 1184;">
<tbody>
<tr>
<td style="border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: blue;">BWA</span><o:p></o:p></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div align="center" class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in; text-align: center;">
<b><span style="font-size: 14.0pt;"><span style="color: blue;">Bowtie</span><o:p></o:p></span></b></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Does not make compromise to memory and
speed usage and guarantees the highest quality reads<o:p></o:p></span></span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Make compromise to memory and speed
usage because it does not guarantee the highest quality read mapping if no
exact match exists.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">It fails to align some reads with
valid mapping when it opts for maximum speed.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<br /></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">uses
mapping quality</span></b><span style="font-size: 12.0pt;"> accepts or rejects
an alignment based on counting the number of mismatches between reads and
corresponding genomic position.<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 12.0pt;">Uses
a quality threshold</span></b><span style="font-size: 12.0pt;"> (alignment
score) to perform same function<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">BWA uses large memory due to mapping
step and 40% slower<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Uses less memory and is 40% fast in
doing alignment <o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Supports alignment when there are some
gaps and mismatches in single end sequence/ alignment<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">No gapped alignment. If the subject
genome has a gap with respect to reference genome it is unlikely to report
the correct alignment for a read<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Memory efficient aligner with low
speed as compared to Bowtie<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Ultrafast and memory efficient aligner<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Uses FM indexing and Burrows Wheeler
Transform algorithm<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Bowtie index is a refinement of FM
Index (Ferragina and Manzini 2000) which in turn uses the Burrows-Wheeler
Transform <o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">No built-in indexes are available with
BWA package<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Built-in indexes are also available
with Bowtie package<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Common method for FM Indexing is the
exact matching algorithm and it does not use double indexing strategy. It
also uses inexact matching (backtracking algorithm but it is not optimal<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Uses <span style="background: white;">double
indexing', a strategy to avoid excessive backtracking. The Bowtie aligner
follows a policy similar to Maq's, in that it allows a small number of
mismatches within the high-quality end of each read, and it places an upper
limit on the sum of the quality values at mismatched alignment positions.</span><o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">It does not reduce the search space by
bounding the search with D(i), where D(i) is the lower bound of differences
in given reads W (0, i)<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">It does not reduce the search space by
bounding the search with D(i), but cleverly doing the alignment for both
original and reversed read sequences to bypass unnecessary searches towards
the root of prefix trie<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">BWA implements breadth-first search
(BFS) so its slower than bowtie<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">By default, Bowtie performs a depth
first search (DFS) on prefix trie and stops when qualified hit is found<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">No possibility to make BWA perform DFS<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">It is possible to make bowtie perform
a BFS by applying <b>-best </b>option at
the command line but this makes bowtie slower<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Generates mapping qualities<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Generates quality scores<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">More accurate in terms of confident
mapping and error rate of confident mapping<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Less accurate in terms of confident
mapping<o:p></o:p></span></span></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">It checks suboptimal hits that’s why
it is slow<o:p></o:p></span></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 233.75pt;" valign="top" width="312"><div class="MsoNormal" style="line-height: normal; margin-bottom: .0001pt; margin-bottom: 0in;">
<span style="font-size: 12.0pt;"><span style="font-family: "verdana" , sans-serif;">Do not check suboptimal hits that’s
why it is fast</span></span></div>
</td>
</tr>
</tbody></table>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com4Park Road، Islamabad 45550, Pakistan33.6518263 73.1565932999999433.4403853 72.833869799999945 33.863267300000004 73.479316799999935tag:blogger.com,1999:blog-7587796149281043589.post-38441231249487777162017-04-25T23:36:00.000-07:002017-04-25T23:36:09.230-07:00Major platforms of Next generation sequencing<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoListParagraphCxSpFirst" style="text-align: left; text-indent: -0.25in;">
<span style="color: purple;"><b><span style="font-size: 7pt; font-stretch: normal; font-variant-numeric: normal; font-weight: normal; line-height: normal;"> </span></b><!--[endif]--></span><b><span style="font-family: "verdana" , sans-serif;"><span style="color: purple;">Illumina sequencing</span><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;">Illumina
platform was first introduced by Solexa in 2006 later re-branded by Illumina.
Two of the major platforms of illumine are HiSeq, MiSeq. This technology
utilizes sequencing by synthesis approach where adapter ligated template
molecules flow into flow cells made glass hollow from inside. Template
hybridizes to primer on the flow cell surface and gets copied onto the flow cell.
Basically, bridge amplification occurs which results in a generation of reverse
complimentary copies of the template. Each cluster holds approximately 1
million copies of the original fragment. Each nucleotide added contains a base
specific fluorescently labelled probe with chemically blocked OH group. The
fluorescently labelled probe is probe is helpful in detection of nucleotide s being incorporated. These incorporated nucleotide s are then imaged using CCD
camera and then DNA Polymerase removes 3’ block chemically to prepare each
strand for next incorporation.<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2LR_T6p0HHEzjabHGI-oCQ3f-YKEc0tFs9x1RRYcH8xDthyphenhyphensj0-T4B8p4CQbW2bGd3PWdmaGC_kwxm3B6fMAVZByYQSrAYp7s-XMW47BKY3mAztVx_WHXQfXRhahNAfsKTjvn_sAOMu0/s1600/web-graphics-hiseq2500-real.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="253" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2LR_T6p0HHEzjabHGI-oCQ3f-YKEc0tFs9x1RRYcH8xDthyphenhyphensj0-T4B8p4CQbW2bGd3PWdmaGC_kwxm3B6fMAVZByYQSrAYp7s-XMW47BKY3mAztVx_WHXQfXRhahNAfsKTjvn_sAOMu0/s320/web-graphics-hiseq2500-real.png" width="320" /></a></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;"><br /></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: left; text-indent: -0.25in;">
<span style="font-family: "verdana" , sans-serif;"><span style="color: purple;"><b><span style="font-size: 7pt; font-stretch: normal; font-variant-numeric: normal; font-weight: normal; line-height: normal;"> </span></b><!--[endif]--></span><b><span style="color: purple;">454 Sequencing/Roche</span><o:p></o:p></b></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;">Roche technology
became commercialized in the year 2005 which uses bead based em-PCR (Emulsion
PCR) approach to amplify the copies of template of DNA molecule. Later these
beads are sequenced by pyrosequencing in parallel fashion. Pyrosequencing
involves four different nucleotides flowed in sequential manner through solid
surface wells, known as picotiter plates into which single bead is
incorporated. Pyrosequencing is based on principle of generation of light
signal through release of pyrophosphate (PPi) on each nucleotide incorporation.
The signal intensity per nucleotide is recorded for each bead and later
analyzed by CCD camera attached to computer system to detect the exact
sequence.<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDG7FCJaP-A7uYKlhoMBwl-ilQ8qmaey1beLF6p5dM3LcdKTujHGxpYvd2YUL6se-4RwSvwRjvVTbyjbS0GtCmEbyTYtAORpITaXEOrzIlNr2iHbSY4ZAgpDab_2JxHDaTWMjy2m86MQM/s1600/Genome-Sequencer-FLX-System1-150x150.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDG7FCJaP-A7uYKlhoMBwl-ilQ8qmaey1beLF6p5dM3LcdKTujHGxpYvd2YUL6se-4RwSvwRjvVTbyjbS0GtCmEbyTYtAORpITaXEOrzIlNr2iHbSY4ZAgpDab_2JxHDaTWMjy2m86MQM/s200/Genome-Sequencer-FLX-System1-150x150.jpg" width="200" /></a></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;"><br /></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: left; text-indent: -0.25in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 7pt; font-stretch: normal; font-variant-numeric: normal; font-weight: normal; line-height: normal;"> <span style="color: purple;"> </span></span></b><!--[endif]--><b><span style="color: purple;">ABI SOLiD</span><o:p></o:p></b></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;">Sequencing by
Oligonucleotide Ligation and Detection is developed by life technologies and
has been commercially available in the year 2006. This Technology is similar to
Roche technology but the only difference is that the beads in SOLiD are smaller
as compared to Roche sequencers. A library of DNA fragments is used to prepare
clonal bead populations. Only one fragment with universal adapter is present on
each bead so that the starting sequence of every fragment is both known and
identical.<span style="background: white; color: #252525;"> The resulting PCR products attached to the beads are then covalently
bound to a glass slide. Primers hybridize to the adapter sequence within the
library template. Later a set of four fluorescently labelled probes of 16
dinucleotide groupings compete for ligation for the sequencing primer. The
nucleotides are recognized by analyzing the color light emitted as a result of
two consecutive ligation reactions. One of the drawback of this system is the
issues with sequencing palindromic sequences.</span><o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjk1NksSdipuWtcSl4nGc05ms8ZeJ5qs3gFl8y1fk4OyT5jBlckRfR1KNOnrCdBu4Io2WFGooe5dUhjtpx33pl6opMR_PvaZfNz9TKeQJEvMWOpo23EBOGezd-H3154FHcW0Ri_4yAx2i0/s1600/BTN_A_000113371_O_F0_85091b.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjk1NksSdipuWtcSl4nGc05ms8ZeJ5qs3gFl8y1fk4OyT5jBlckRfR1KNOnrCdBu4Io2WFGooe5dUhjtpx33pl6opMR_PvaZfNz9TKeQJEvMWOpo23EBOGezd-H3154FHcW0Ri_4yAx2i0/s1600/BTN_A_000113371_O_F0_85091b.jpg" /></a></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: justify;">
<span style="font-family: "verdana" , sans-serif;"><span style="background: white; color: #252525;"><br /></span></span></div>
<div class="MsoListParagraphCxSpLast" style="text-align: left; text-indent: -0.25in;">
<span style="font-family: "verdana" , sans-serif;"><b><span style="font-size: 7pt; font-stretch: normal; font-variant-numeric: normal; font-weight: normal; line-height: normal;"> <span style="color: purple;"> </span></span></b><!--[endif]--><b><span style="color: purple;">Ion Torrent</span><o:p></o:p></b></span></div>
<div class="MsoListParagraphCxSpLast" style="text-align: left; text-indent: -0.25in;">
<span style="font-family: "verdana" , sans-serif;"><b><br /></b></span></div>
<div style="text-align: left;">
<span style="font-family: "verdana" , sans-serif;"><span style="line-height: 107%;">Ion semiconductor sequencing is based on the
detection of hydrogen ions that are released during polymerization of DNA by
using sequencing by synthesis approach. Ion torrent detects the nucleotide's and
then converts them into digital format 1 and 0 on a semiconductor chip. When a
nucleotide is incorporated in the strand of DNA, H+ ion is released which is
detected by semiconductor chip. The charge from the ion will change the PH, of
solution which can be detected in the form of peaks by i</span><span style="line-height: 107%;">on sensor.</span></span></div>
<div style="text-align: left;">
<span style="font-family: "calibri" , sans-serif; font-size: 11.0pt; line-height: 107%;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRsDNuSws0Gx8VBUhhnTCkQ5R9o6U4EicJ3cIc_ZeRxSUcVUcl_fHSaWsNmTim62rI8slKzXBejiFS-U1zIEnL71KyA-SeHtHRjmBUHzk0lL-sbGUuJBHBv0hHIMkpFLTKf8hyphenhyphenVyfCN9I/s1600/download.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRsDNuSws0Gx8VBUhhnTCkQ5R9o6U4EicJ3cIc_ZeRxSUcVUcl_fHSaWsNmTim62rI8slKzXBejiFS-U1zIEnL71KyA-SeHtHRjmBUHzk0lL-sbGUuJBHBv0hHIMkpFLTKf8hyphenhyphenVyfCN9I/s1600/download.jpg" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div style="text-align: left;">
<span style="font-family: "calibri" , sans-serif; font-size: 11.0pt; line-height: 107%;"><br /></span></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-17639055314471100322016-06-16T15:36:00.000-07:002016-06-16T15:36:27.335-07:00FastQC tool<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: left;">
<span style="font-family: "verdana" , sans-serif;">FastQC is a quality control tool for checking the quality of raw reads obtained from Next Generation sequencing platforms. It provides a modular set of analysis which gives a quick hint of quality of your data. It generates QC report in the form of graphs showing quality, N content, Adapter content, GC content present in your high throughput sequencing data. It can be downloaded from (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).<br />FastQC can be run in different modes which are</span></div>
<ul style="text-align: left;">
<li><span style="font-family: "verdana" , sans-serif;">Standalone interactive application</span></li>
</ul>
<ul style="text-align: left;">
<li><span style="font-family: "verdana" , sans-serif;">Non interactive mode</span></li>
<li><span style="font-family: "verdana" , sans-serif;">By using galaxy which contains integrated FastQC tool</span></li>
</ul>
<h3 style="text-align: left;">
<span style="color: purple; font-family: "verdana" , sans-serif;">Working</span></h3>
<br />
<div style="text-align: left;">
<span style="font-family: "verdana" , sans-serif;">1) Install the FastQC from above mentioned link. It can be installed on both LINUX as well as windows operating system. on linux it can be installed by using command </span></div>
<div style="text-align: left;">
<span style="font-family: "verdana" , sans-serif;"> </span><span style="font-family: "courier new" , "courier" , monospace;">sudo apt-get [link of fastQC from where you are downloading]</span></div>
<div style="text-align: left;">
<span style="background-color: white; color: #333333; line-height: 16.8px; white-space: pre;"><span style="font-family: "courier new" , "courier" , monospace;"> sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc</span></span></div>
<div style="text-align: left;">
<span style="font-family: "courier new" , "courier" , monospace;"><span style="background-color: white; color: #333333; line-height: 16.8px; white-space: pre;"> </span><span style="background-color: white; color: #333333; line-height: 16.8px; white-space: pre;">fastqc somefile.txt</span></span></div>
<div style="text-align: left;">
<span style="font-family: "verdana" , sans-serif;"><span style="background-color: white; color: #333333; line-height: 16.8px; white-space: pre;">2) After installing FastQC now simply run the program and select </span>File > Open. You can then select the files you want to analyse by using windows. But in LINUX use following command</span></div>
<div style="text-align: left;">
<span style="background-color: white; color: #333333; font-family: "courier new" , "courier" , monospace; line-height: 16.8px; white-space: pre;"> fastqc somefile.txt</span></div>
<div style="font-family: sans-serif;">
FastQC supports files in the following formats</div>
<ul style="font-family: sans-serif;">
<li>FastQ (all quality encoding variants)</li>
<li>Casava FastQ files*</li>
<li>Colorspace FastQ</li>
<li>GZip compressed FastQ</li>
<li>SAM</li>
<li>BAM</li>
<li>SAM/BAM</li>
</ul>
<span style="font-family: sans-serif;">The analysis in FastQC is performed by a series of analysis modules. The left hand side of the main interactive display or the top of the HTML report show a summary of the modules which were run, and a quick evaluation of whether the results of the module seem entirely normal (green tick), slightly abnormal (orange triangle) or very unusual (red cross).</span><br />
<div>
<span style="font-family: sans-serif;">Shown below are some results obtained from FastQC</span></div>
<div>
<span style="font-family: sans-serif;"><br /></span></div>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIf6WQssi3EytToA-kd_pxxc67MysF0XRm288vUIR32NSDMMxZyXpQmX2K77xoNXSGJuQV-QffZan4HPpIIhQDfSvOV49iN1JdL_sMqYIXKjooQatl7kMwIeVZgCB8vcqDNCvB3Yb7PgE/s1600/fastqc.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="273" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIf6WQssi3EytToA-kd_pxxc67MysF0XRm288vUIR32NSDMMxZyXpQmX2K77xoNXSGJuQV-QffZan4HPpIIhQDfSvOV49iN1JdL_sMqYIXKjooQatl7kMwIeVZgCB8vcqDNCvB3Yb7PgE/s400/fastqc.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Summary report FastQC<br />
<div style="text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmqJgjiGNtIihawTuh09I422UVvkGDKH-bCOTKkuKG9c_Awh2_IA-oo8Ly9rUZJ3es3aSEHYNwyYLT0e7DtLhSpaioKrD5t81nTRHHrYINcRv4MS0KWaCljA-LnTPUBo8ZpFRvl4UyP1s/s1600/K1rDMeq.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmqJgjiGNtIihawTuh09I422UVvkGDKH-bCOTKkuKG9c_Awh2_IA-oo8Ly9rUZJ3es3aSEHYNwyYLT0e7DtLhSpaioKrD5t81nTRHHrYINcRv4MS0KWaCljA-LnTPUBo8ZpFRvl4UyP1s/s400/K1rDMeq.png" width="400" /></a></div>
<div style="text-align: left;">
<br /></div>
<div style="text-align: left;">
<span style="font-size: small;"><span style="font-family: "verdana" , sans-serif;"><br /></span></span></div>
<div style="text-align: left;">
<span style="font-size: small;"><span style="font-family: "verdana" , sans-serif;">Now after generation of report click on the options showing on left of the windows to get other details like N content, Adapter content, GC content and many more in graphical format. </span><span style="font-family: "verdana" , sans-serif;">The quality control step is the first step of Next Generation Sequencing data analysis. These graps shows the complete report about quality of the raw reads. Any reads that do not meet the quality are Trimmed off Using any of the poor quality reads trimming tools. To know about the trimming tools stay connected and visit the blog.</span><span style="font-family: "verdana" , sans-serif;"><br /></span><span style="font-family: "verdana" , sans-serif;"><br /></span></span></div>
</td></tr>
</tbody></table>
<span style="font-family: "verdana" , sans-serif;"><br /></span>
<a href="http://www.clixsense.com/?9325259" target=_blank><img src="https://csstatic.com/banners/clixsense_gpt468x60a.png" border="0"></a>
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<div>
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179472 72.770422600000018 33.9408292 73.415869600000008tag:blogger.com,1999:blog-7587796149281043589.post-22401593986972004022016-06-15T05:06:00.000-07:002016-06-15T05:06:06.473-07:00Interactive genome viewer (IGV)<div dir="ltr" style="text-align: left;" trbidi="on">
Interactive Genome Viewer is a high performance, powerful visualization tool for large genomic data sets. It supports a wide variety of data types such as<br />
<br />
<ul style="text-align: left;">
<li>Next generation sequencing data</li>
<li>SAM files</li>
<li>Array based data</li>
<li>other genomic data sets</li>
</ul>
<div style="text-align: justify;">
IGV is a basic data visualization and exploration tool such as whole exome sequencing data, whole genome sequencing data and much more.<span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;">IGV is freely available for download from </span><a href="http://www.broadinstitute.org/igv" style="background-color: white; border: 0px; color: #0000cc; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px; margin: 0px; outline-style: none; padding: 0px; text-decoration: none; vertical-align: baseline;">http://www.broadinstitute.org/igv</a><span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;">, under a GNU LGPL open-source license. IGV is a desktop application written in JAVA Programming language and works on many platforms like windows, MAC and LINUX.</span></div>
<div style="text-align: justify;">
<span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px; text-align: left;">A primary design goal of IGV is to support interactive exploration of large-scale genomic data sets on standard desktop computers. It supports multiple file formats for genomic data such as</span></div>
<div style="text-align: justify;">
<ul>
<li><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="font-size: 14px; line-height: 21px;">BED</span></span></li>
<li><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="font-size: 14px; line-height: 21px;">BAM</span></span></li>
<li><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="font-size: 14px; line-height: 21px;">SNP files</span></span></li>
</ul>
<span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px; text-align: left;">It allows investigators to visualize many different types of data together—and importantly also integrate these data with the display of sample attribute information such as clinical and phenotypic information. To support interactive exploration of data, IGV provides direct manipulation navigation in the style of Google Maps. For instance, you click and drag to pan the view across the genome and double-click on a region to zoom in for a more detailed view. It supports real-time interaction at all scales of genome resolution, from whole genome to base pairs, even for very large data sets. The Broad IGV data server hosts many genome annotation files and data sets from a variety of public sources (including from TCGA, 1000 Genomes Project, ENCODE Project </span><span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px; text-align: left;"> and others). </span></div>
<h2 style="text-align: left;">
<span style="color: purple; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>Step by step procedure to visualize genomic reads</b></span></span></h2>
<div>
<span style="color: #274e13;"><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>1) Install IGV on your computers by downloading it from (</b></span></span><a href="http://www.broadinstitute.org/igv" style="background-color: white; border: 0px; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px; margin: 0px; outline-style: none; padding: 0px; text-decoration: none; vertical-align: baseline;">www.broadinstitute.org/igv</a><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;">)</span></span></span></div>
<div>
<span style="color: #274e13; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>2) Get familiar with the control pane of IGV windows</b></span></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXH8IKAoKq0jtxVaiddqCmlDePukPNHWXfkH6coRFasr8LJyk0Is3KXcVi_m1_Ii7D-YoJqzqlVAXnAsCb3twUdssM4vEyfIGAQJXA6KoQlCQ1qXjLlnYiuXQLpCZDzC4MwbkCXGwRuCc/s1600/F2.large.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="270" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXH8IKAoKq0jtxVaiddqCmlDePukPNHWXfkH6coRFasr8LJyk0Is3KXcVi_m1_Ii7D-YoJqzqlVAXnAsCb3twUdssM4vEyfIGAQJXA6KoQlCQ1qXjLlnYiuXQLpCZDzC4MwbkCXGwRuCc/s400/F2.large.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">IGV windows<br /></td></tr>
</tbody></table>
<div>
<span style="color: #274e13;"><span style="font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>3) Select the reference genome before loading the data. select genome option is given in toolbar at the top of IGV window.</b></span></span><b><span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span><span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;">IGV provides dozens of hosted reference genomes to choose from, but also provides the option of importing others from the sequence data. The minimal requirement for importing a genome is a FASTA file containing chromosome or contig sequences.</span><span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;"> </span></b></span></div>
<div>
<span style="color: #274e13; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>4) Now load your genomic data</b></span></span></div>
<div>
<span style="color: #274e13; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>5)After aligning the reads on reference genome of interest visualize the alignment.</b></span></span></div>
<div>
<span style="color: #274e13; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>7) Visualize the insertions, deletions and SNP,s along with their Allele frequencies and details of amino acid changes.</b></span></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj-MY8-cvsqL46k9ONyRJKmg8Eiayqfawim1YoHszdsWRpKz_cF6vTie_b7dUGRelMUYbKAxHl9jKOcTAkU9rOkCF3A-aQZOLZJCpKNlVVRHsNAf976Jgfa3n_c8j8UalrVXR-89UmCNk/s1600/F4.large.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj-MY8-cvsqL46k9ONyRJKmg8Eiayqfawim1YoHszdsWRpKz_cF6vTie_b7dUGRelMUYbKAxHl9jKOcTAkU9rOkCF3A-aQZOLZJCpKNlVVRHsNAf976Jgfa3n_c8j8UalrVXR-89UmCNk/s400/F4.large.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Alignment on reference genome and visualization of both reverse and forward strands<br /></td></tr>
</tbody></table>
<div>
<span style="color: magenta; font-family: Lucida Grande, Lucida Sans Unicode, Tahoma, Verdana, Arial, Helvetica, sans-serif;"><span style="background-color: white; font-size: 14px; line-height: 21px;"><b>For any queries regarding its working feel free to comment :)</b></span></span></div>
<div style="text-align: justify;">
<span style="background-color: white; font-family: "Lucida Grande", "Lucida Sans Unicode", Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 14px; line-height: 21px;"><br /></span></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Southern Asia25.03764 76.456308700000022-28.319115 -6.1608787999999777 78.394395 159.07349620000002tag:blogger.com,1999:blog-7587796149281043589.post-34886582835160777932016-05-30T02:24:00.001-07:002016-05-30T02:24:02.197-07:00Galaxy tool <div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;"><b style="background-color: white; box-sizing: border-box; line-height: 25.2px;">Galaxy</b><span style="background-color: white;"><span style="line-height: 25.2px;"> is an open source, web-based platform for data intensive bio medical research. It </span></span><span style="background-color: white; line-height: 22.4px;">is a </span><span style="color: black;">scientific workflow<span style="background-color: white; line-height: 22.4px;">, </span>data integration<span style="background-color: white; line-height: 22.4px;">,</span><span style="background-color: white; line-height: 22.4px;"> and </span>data and analysis persistence and publishing</span><span style="background-color: white; line-height: 22.4px;"> platform that aims to make </span>computational biology<span style="background-color: white; line-height: 22.4px;"> accessible to research scientists that do not have </span>computer programming<span style="background-color: white; line-height: 22.4px;"> experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general </span><span style="color: black;">bioinformatics workflow management system<span style="background-color: white; line-height: 22.4px;">.</span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;"><span style="color: black;"><span style="background-color: white; line-height: 22.4px;"><br /></span></span></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6ONA-PDIxoGmdyl-KzH8FsrVwcoL_GWzv4SMmiOyzJVPE3huHsb3sVsBxpBkK1bgKsG6GU8rQlPOhIAUED3LWqsTLIxQQVhA_hPEvFSwdHBJQ-5TGzkOvJCRj4HEmUgV99Jjb-7ObIiQ/s1600/Capture.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="296" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6ONA-PDIxoGmdyl-KzH8FsrVwcoL_GWzv4SMmiOyzJVPE3huHsb3sVsBxpBkK1bgKsG6GU8rQlPOhIAUED3LWqsTLIxQQVhA_hPEvFSwdHBJQ-5TGzkOvJCRj4HEmUgV99Jjb-7ObIiQ/s640/Capture.PNG" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Galaxy snapshot</td></tr>
</tbody></table>
<div style="text-align: center;">
<br /></div>
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;"><span style="color: black;"><span style="background-color: white; line-height: 22.4px;"><br /></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;"><span style="background-color: white; line-height: 22.4px; text-align: start;">Galaxy is also a </span>data integration<span style="background-color: white; line-height: 22.4px; text-align: start;"> platform for biological data. It supports data uploads from the user's computer, by URL, and directly from many online resources (such as the </span>UCSC Genome Browser<span style="background-color: white; line-height: 22.4px; text-align: start;">, </span>BioMart<span style="background-color: white; line-height: 22.4px; text-align: start;"> and </span>InterMine<span style="background-color: white; line-height: 22.4px; text-align: start;">). Galaxy supports a range of widely used </span>biological data formats<span style="background-color: white; line-height: 22.4px; text-align: start;">, and translation between those formats. Galaxy provides a web interface to many text manipulation utilities, enabling researchers to do their own custom reformatting and manipulation without having to do any </span>programming.</span></div>
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;">It provides workflows to do </span></div>
<div style="text-align: justify;">
</div>
<ul>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">NGS analysis</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">Targeted genome analysis</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">whole genome analysis</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">variant discovery</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">ChiP-seq Analysis</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">gene expression studies</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">De novo genome assembly</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">SNP and Indel detection</span></b></span></li>
<li><span style="font-family: Verdana, sans-serif;"><b><span style="color: orange;">Genomic resequencing Variant detection</span></b></span></li>
</ul>
<br />
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179472 72.770422600000018 33.9408292 73.415869600000008tag:blogger.com,1999:blog-7587796149281043589.post-61226247506516625282015-12-05T11:11:00.000-08:002015-12-05T11:11:57.499-08:00CRISPR Cas 9 technology (A novel DNA modification system for Genome editing/ Genome Engineering)<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal">
<b><u><span style="font-size: 16.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Introduction<o:p></o:p></span></span></u></b></div>
<span style="font-family: Verdana, sans-serif;"><span style="background: white; font-size: 13pt; line-height: 115%;">The<span class="apple-converted-space"> </span>CRISPR/Cas system<span class="apple-converted-space"> </span>is a<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">prokaryotic</span></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">immune system</span></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">that confers resistance to foreign genetic
elements such as<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Plasmids" title="Plasmids"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">plasmids</span></a></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">and<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">phages</span></span><span style="background: white; font-size: 13pt; line-height: 115%;">,<span class="apple-converted-space"> </span>and
provides a form of </span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">acquired immunity</span></span><span style="background: white; font-size: 13pt; line-height: 115%;">. CRISPR spacers recognize and cut these
exogenous genetic elements in a manner analogous to </span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/RNAi" title="RNAi"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">RNAi</span></a></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">in<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Eukaryote" title="Eukaryote"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">eukaryotic</span></a></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">organisms.<span class="apple-converted-space"> </span>CRISPRs
are found in approximately 40% of sequenced<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">bacteria</span></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">genomes and 90% of sequenced </span><span style="font-size: 11pt; line-height: 115%;"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">archaea</span></span><span style="background: white; font-size: 13pt; line-height: 115%;">.</span></span><br />
<span style="font-family: Verdana, sans-serif;"><span style="background: white; font-size: 13pt; line-height: 115%;"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;">Clustered regularly
interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas)
proteins are found in many bacteria and most archaea. The CRISPR-Cas systems
use sequences derived from plasmids and phages to activate Cas endonucleases to
neutralize those plasmids and phages via RNA-guided sequence-specific DNA
cleavage, thus blocking their transmission and creating a simple acquired
immunity.</span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;"> The CRISPR/Cas system has
been used for<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Genome_engineering"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext; font-size: 13pt; line-height: 115%; text-decoration: none;">gene editing</span></a></span><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;">(adding, disrupting or changing the sequence of
specific genes) and gene regulation in species throughout the </span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Tree_of_life_(biology)"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext; font-size: 13pt; line-height: 115%; text-decoration: none;">tree of life</span></a></span><b><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;">.</span></b></span><span style="background: white; font-size: 13pt; line-height: 115%;">By delivering the<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Cas9"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">Cas9</span></a></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">protein and appropriate guide RNAs into a cell,
the organism's<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Genome"><span style="background: white; color: windowtext; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial; text-decoration: none; text-underline: none;">genome</span></a></span><span class="apple-converted-space"><span style="background: white; font-size: 13pt; line-height: 115%;"> </span></span><span style="background: white; font-size: 13pt; line-height: 115%;">can be relatively cheaply cut at any desired
location<b>.</b></span><span style="background-color: white; font-size: 13pt; line-height: 115%;">CRISPR has a number of
potential applications including treating genetic diseases, fighting
infections, and increasing food crop yields, but the application of this method
is accompanied by ethical concerns.</span></span><br />
<span style="background: white; font-size: 13pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> </span><div class="separator" style="clear: both; font-family: Calibri, sans-serif; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbmYF4qxujXfG-mYSsrj90GKW-Ua4g78ADyoqtsYFmZ4OGihKMzsGtpJ8lDU8GvbT5bSjqEzcVukbHve0msFLGVVGxpl_uluxpEJpU0pUge2V70wQmCX68IVIC8MZldqHn3ajNbrLa6jo/s1600/crispr-cas9-CO013130.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="238" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbmYF4qxujXfG-mYSsrj90GKW-Ua4g78ADyoqtsYFmZ4OGihKMzsGtpJ8lDU8GvbT5bSjqEzcVukbHve0msFLGVVGxpl_uluxpEJpU0pUge2V70wQmCX68IVIC8MZldqHn3ajNbrLa6jo/s320/crispr-cas9-CO013130.png" width="320" /></a></div>
<div class="MsoNormal" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; line-height: normal; margin-bottom: 0.1in;">
<b><u><span style="font-size: 16pt;"><span style="font-family: Verdana, sans-serif;">The
CRISPR/Cas9 system for targeted genome editing<o:p></o:p></span></span></u></b></div>
<div class="MsoNormal" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; line-height: normal; margin-bottom: 0.1in;">
<span style="font-family: Verdana, sans-serif;"><span style="font-size: 13pt; line-height: 115%;">Although recently-developed
programmable editing tools, such as zinc finger nucleases and transcription
activator-like effectors nucleases, have significantly improved the capacity
for precise genome modification, these techniques have limitations. CRISPR (clustered
regularly interspaced short palindromic repeats)/Cas9 technology represents a
significant improvement over these other next-generation genome editing tools,
reaching a new level of targeting, efficiency, and ease of use. The CRISPR/Cas9
system allows for site-specific genomic targeting in virtually any organism.</span><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: #333333; font-size: 13pt; line-height: 115%;"> </span></span></span></div>
<div class="MsoNormal" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; line-height: normal; margin-bottom: 0.1in;">
<span style="font-size: 13pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">The type II CRISPR/Cas system is a prokaryotic adaptive
immune response system that uses non-coding RNAs to guide the Cas9 nuclease to
induce site-specific DNA cleavage. This DNA damage is repaired by cellular DNA
repair mechanisms, either via the non-homologous end joining DNA repair pathway
(NHEJ) or the homology directed repair (HDR) pathway.<span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span></span></span></div>
<div style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">
<span style="font-family: Verdana, sans-serif;"><span style="font-size: 13pt;">The CRISPR/Cas9 system has been harnessed to create a
simple, RNA-programmable method to mediate genome editing in mammalian cells,
and can be used to generate gene knockouts (via insertion/deletion) or knockins
(via HDR). To create gene disruptions <b>(Figure
1),</b> a single guide RNA (sgRNA) is generated to direct the Cas9 nuclease to
a specific genomic location. Cas9-induced double strand breaks are repaired via
the NHEJ DNA repair pathway. The repair is error prone, and thus insertions and
deletions (INDELs) may be introduced that can disrupt gene function.</span><b><o:p></o:p></b></span></div>
<div style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">
<span style="font-size: 13pt;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: Verdana, sans-serif;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0OK-ZW4ZuIxNJrnTwwKhwCa-6ooG-LAACSDT5Id93JBmL3HgZl_Z2fueJLMtSSfmxxYQPYbr7BHR9G6v6phawEPSAg4WxC8i9SF6cM74HWgPDbCe5ja6aepgfbMfQHaiPn1G6TxQOaME/s1600/download.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="271" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0OK-ZW4ZuIxNJrnTwwKhwCa-6ooG-LAACSDT5Id93JBmL3HgZl_Z2fueJLMtSSfmxxYQPYbr7BHR9G6v6phawEPSAg4WxC8i9SF6cM74HWgPDbCe5ja6aepgfbMfQHaiPn1G6TxQOaME/s400/download.jpg" width="400" /></a></span></div>
</span><br />
<div style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">
<span style="font-size: 13pt;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
<div style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">
<span style="font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;">Targeted genome editing
using engineered nucleases has rapidly gone from being a niche technology to a
mainstream method used by many biological researchers. This widespread adoption
has been largely fueled by the emergence of the clustered, regularly
interspaced, short palindromic repeat (CRISPR) technology, an important new
approach for generating RNA-guided nucleases, such as Cas9, with customizable
specificities.</span><span style="font-size: 13pt; line-height: 115%;">Genome editing mediated by
these nucleases has been used to rapidly, easily and efficiently modify
endogenous genes in a wide variety of biomedically important cell types and in
organisms that have traditionally been challenging to manipulate genetically. Furthermore,
a modified version of the CRISPR-Cas9 system has been developed to recruit heterogonous
domains that can regulate endogenous gene expression or label specific genomic
loci in living cells. Although the genome-wide specificities of CRISPR-Cas9
systems remain to be fully defined, the power of these systems to perform
targeted, highly efficient alterations of genome sequence and gene </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;">expression will undoubtedly
transform biological research and spur the development of novel molecular
therapeutics for human disease.<span class="apple-converted-space"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 13pt; line-height: 115%;"> </span><b style="background-color: transparent;"><u><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 16pt; line-height: 115%;">Role of CRISPR in Gene therapy</span></u></b></span></div>
<div class="MsoNormal">
<span style="font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;"><span style="font-family: Verdana, sans-serif;">Gene therapy involves manipulating DNA or RNA for human disease
treatment or prevention. The strategies of gene therapy are diverse, such as
rectifying, replacing or deleting the culprit genes in genetic diseases, producing
disabling mutations in pathogen genomes to combat infectious diseases or
inducing therapeutic or protective somatic mutations. It is a promising therapy
for a wide range of human diseases including hematological diseases,<span class="apple-converted-space"> </span>cancer, AIDS,<span class="apple-converted-space"> </span>diabetes,<span class="apple-converted-space"> </span>heart failure,<span class="apple-converted-space"> </span>and neurodegenerative diseases.<o:p></o:p></span></span></div>
<h3 style="margin: 11.25pt 0in 1.5pt 3.75pt; vertical-align: baseline;">
<span style="color: windowtext; font-size: 16pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Correcting
monogenic disorders<o:p></o:p></span></span></h3>
<div class="MsoNormal">
<span style="font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;"><span style="font-family: Verdana, sans-serif;">Monogenetic disorder is caused by single gene defects. Compared with
polygenic diseases such as cancer, monogenic disorders are more amenable to
gene therapies. Currently, the correction of monogenic disorders represents the
most translatable field in CRISPR-Cas9-mediated gene therapy.<o:p></o:p></span></span></div>
<h4 style="margin: 11.25pt 0in 1.5pt 3.75pt; vertical-align: baseline;">
<span style="font-size: 14pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Somatic gene correction in adult
animals<span style="color: #333333;"><o:p></o:p></span></span></span></h4>
<span style="font-size: 13pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">CRISPR-Cas9 technology can also mediate somatic gene
corrections in adult animals, bypassing embryo manipulations. [<b>Yin</b><span class="apple-converted-space"> </span><em><b><span style="border: 1pt none windowtext; padding: 0in;">et al</span></b></em><b>,]</b><span class="apple-converted-space"> </span>for example, delivered CRISPR-Cas9
agents and a homologous donor template (in order to increase HDR rate) into
adult mice with hereditary tyrosinemia via tail-vein hydrodynamic injection,
resulting in gene corrections in 0.25% of liver cells initially, and in 33.5%
of liver cells 33 days post injection (possibly due to selective advantages
imposed by the correction), which was sufficient to rescue the disease
phenotype. This method is more translatable to human therapeutics because it
does not involve embryo manipulations.</span></span><div>
<div class="MsoNormal">
<b><u><span style="font-size: 16.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Applications<o:p></o:p></span></span></u></b></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">The technology has been used to functionally inactivate
genes in human cell lines and cells, to study<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Candida_albicans"><i><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">Candida albicans</span></i></a><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">, to modify<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Yeasts"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">yeasts</span></a><span class="apple-converted-space"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;"> </span></span><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">used to make<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Biofuels"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">biofuels</span></a><span class="apple-converted-space"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;"> </span></span><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">and to<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Genetically_modified_crops"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">genetically modify crop</span></a><span class="apple-converted-space"><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;"> </span></span><span style="background: white; font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">strains<o:p></o:p></span></span></div>
<div style="background: white; margin-top: .05in;">
<span class="mw-headline"><span style="font-size: 14.5pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Editing</span></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 6.0pt; margin-left: 0in; margin-right: 0in; margin-top: 6.0pt;">
<span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"><span style="font-family: Verdana, sans-serif;">CRISPRs
can add and delete base pairs at specifically targeted DNA loci and have
been used to cut as many as five genes at once. CRISPR's low cost compared
to alternatives is widely seen as revolutionary. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 6.0pt; margin-left: 0in; margin-right: 0in; margin-top: 6.0pt;">
<span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"><span style="font-family: Verdana, sans-serif;">Selective
engineered redirection of the CRISPR/Cas system was first demonstrated in 2012
in the following applications: <o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; margin-left: 19.2pt; mso-list: l0 level1 lfo1; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="font-size: 10pt;">·<span style="font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";">Immunization of industrially
important bacteria, including some used in food production and large-scale
fermentation<o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; margin-left: 19.2pt; mso-list: l0 level1 lfo1; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="font-size: 10pt;">·<span style="font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";">Cellular or organism RNA-guided </span><a href="https://en.wikipedia.org/wiki/Genome_engineering"><span style="color: windowtext; font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman"; text-decoration: none; text-underline: none;">genome engineering</span></a><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";">. Proof of concept studies demonstrated examples both </span><a href="https://en.wikipedia.org/wiki/In_vitro"><i><span style="color: windowtext; font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman"; text-decoration: none; text-underline: none;">in vitro</span></i></a><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"> and </span><a href="https://en.wikipedia.org/wiki/In_vivo"><i><span style="color: windowtext; font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman"; text-decoration: none; text-underline: none;">in vivo</span></i></a><i><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";">.</span></i><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; margin-left: 19.2pt; mso-list: l0 level1 lfo1; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="font-size: 10pt;">·<span style="font-size: 7pt; font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--></span><span style="font-size: 13.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"><span style="font-family: Verdana, sans-serif;">Bacterial strain discrimination
by comparison of spacer sequences</span><o:p></o:p></span></div>
<h3 style="background: white; margin-top: .05in;">
<span style="font-family: Verdana, sans-serif;"><span class="mw-headline"><span style="font-size: 14.5pt; line-height: 115%;">Reversible knockdown</span></span><span style="font-size: 14.5pt; line-height: 115%;"><o:p></o:p></span></span></h3>
<div style="background: white; line-height: 16.8pt; margin-bottom: 6.0pt; margin-left: 0in; margin-right: 0in; margin-top: 6.0pt;">
<span style="font-size: 13pt;"><span style="font-family: Verdana, sans-serif;">"CRISPRi" like RNAi, turns
off genes in a reversible fashion by targeting but not cutting a site.
RNA-guided CRISPR associated nuclease Cas9 is an effective way of targeting and
silencing specific genes at the DNA level<sup>.</sup>In bacteria, the presence of
Cas9 alone is enough to block transcription, but for mammalian applications, a
section of protein is added. Its guide RNA targets regulatory DNA, called
promoters that immediately precede the gene target. <o:p></o:p></span></span></div>
<h3 style="background: white; margin-top: .05in;">
<span style="font-family: Verdana, sans-serif;"><span class="mw-headline"><span style="color: windowtext; font-size: 14.5pt; line-height: 115%;">Activation</span></span><span style="color: windowtext; font-size: 14.5pt; line-height: 115%;"><o:p></o:p></span></span></h3>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; margin-left: 19.2pt; mso-list: l0 level1 lfo1; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
<span style="font-size: 13pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Cas9 was used to carry synthetic transcription factors
(protein fragments that turn on genes) that activated specific human genes. The
technique achieved a strong effect by targeting multiple CRISPR constructs to
slightly different spots on the gene's promoter<span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">. </span></span></span></div>
<h3 style="background: white; margin-top: .05in;">
<span style="font-family: Verdana, sans-serif;"><span class="mw-headline"><span style="font-size: 14.5pt; line-height: 115%;">Disease models</span></span><span style="font-size: 14.5pt; line-height: 115%;"><o:p></o:p></span></span></h3>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; margin-left: 19.2pt; mso-list: l0 level1 lfo1; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
<span style="font-family: Verdana, sans-serif;"><span style="font-size: 13pt; line-height: 115%;">CRISPR simplifies creation of<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Genetically_modified_organism#Mammals"><span style="font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">animals
for research</span></a></span><span class="apple-converted-space"><span style="font-size: 13pt; line-height: 115%;"> </span></span><span style="font-size: 13pt; line-height: 115%;">that mimic disease or
show what happens when a gene is<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Gene_knockdown"><span style="font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">knocked down</span></a></span><span class="apple-converted-space"><span style="font-size: 13pt; line-height: 115%;"> </span></span><span style="font-size: 13pt; line-height: 115%;">or mutated. CRISPR
may be used at the<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; line-height: 115%;"><a href="https://en.wikipedia.org/wiki/Germline"><span style="font-size: 13.0pt; line-height: 115%; mso-bidi-font-family: Arial;">germ line</span></a></span><span class="apple-converted-space"><span style="font-size: 13pt; line-height: 115%;"> </span></span><span style="font-size: 13pt; line-height: 115%;">level to create
animals where the gene is changed everywhere, or it may be locally targeted</span></span></div>
</div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Gilgit35.8546284 74.49945170000000935.0319269 73.208558200000013 36.677329900000004 75.7903452tag:blogger.com,1999:blog-7587796149281043589.post-36092476160484215062015-10-22T08:38:00.001-07:002015-10-22T08:38:58.600-07:00Introduction with tables using HTML<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="font-family: Verdana, sans-serif;"><html></span><br />
<span style="font-family: Verdana, sans-serif;"><body></span><br />
<span style="font-family: Verdana, sans-serif;"><Table></span><br />
<span style="font-family: Verdana, sans-serif;"><Table border="1" cellpadding"10"></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td><img Src="CIIT.png" height="250" width="400"></td></span><br />
<span style="font-family: Verdana, sans-serif;"> <th colspan="3" bgcolor="lightblue"><FONT COLOR="darkblue" FACE="Geneva, Arial" SIZE=7> Comsats Institute of Information Technology</FONT> </th></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td><img Src="download.jpg"height="300"width="500"></td></span><br />
<span style="font-family: Verdana, sans-serif;"> <td colspan="3" bgcolor="lightgreen"><FONT COLOR="BLACK" FACE="Geneva, Arial" SIZE=3> Comsats is located in chakshehzad islamabad.Comsats Islamabad is </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">offering degree in BS in Computer science, bioinformatics,mathematics bi osciences ,psychology and electrical engineering.Apart from that it is providing </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">degree of masters in mathematics, computer science and electrical engineering.The Commission on Science and Technology for Sustainable Development in the </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">South (COMSATS) is an international organization. It aims to reduce the ever-growing gap between the developed and developing world through useful </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">applications of science and technology. The Third World Academy of Sciences (TWAS) initiated the proposal for the formation of COMSATS under the leadership </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">of Nobel Laureate, Dr. Abdus Salam.</FONT></td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td rowspan="4"bgcolor="lightblue"><FONT COLOR="BLACK" FACE="Geneva, Arial" SIZE=3>Vision:<br></span><br />
<span style="font-family: Verdana, sans-serif;">CIIT aspires to be both one of the top research institutions and one of the best higher education providers in the country. It envisages becoming a </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">university by the name of “COMSATS University”, for which the legal documentation is under process with the Government of Pakistan. The vision being pursued </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">by the CIIT is to become one of the top 100 universities in the developing world. The CIIT further intends to earn a place among the top 500 universities of </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">the world by the year 2020</FONT></td></span><br />
<span style="font-family: Verdana, sans-serif;"> <td colspan="3" bgcolor="lightblue"><FONT COLOR="darkblue" FACE="Geneva, Arial" SIZE=7>CIIT’s Rankings & Reputation<FONT></td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td colspan="3" bgcolor="lightgreen"><FONT COLOR="BLACK" FACE="Geneva, Arial" SIZE=3>International:<BR>CIIT is ranked among top 250 Asian Universities </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">as per QS University Rankings 2014.<BR>CIIT has been awarded three Stars rating out of a total of five by QS Star Rating System in 2013. Besides, five stars </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">have also been awarded to CIIT in Teaching, and Learning, Facilities and Engagement. </FONT></td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td colspan="3"><FONT COLOR="BLACK" FACE="Geneva, Arial" SIZE=3>National:<BR>CIIT has been ranked number 02 in General Category in 2014.<BR>Ranked </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">Number 1 in Computer Science and IT Category in 2012.<BR>CIIT has also been ranked number 04 in overall universities within Pakistan in 2014.</FONT> </td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <td>BS-BIOINFORMATICS</td></span><br />
<span style="font-family: Verdana, sans-serif;"> <td>BS-COMPUTERSCIENCE</td></span><br />
<span style="font-family: Verdana, sans-serif;"> <td>BS-ELECTRICAL ENGINEERING</td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr></span><br />
<br />
<span style="font-family: Verdana, sans-serif;"></Table></span><br />
<span style="font-family: Verdana, sans-serif;"></body></span><br />
<span style="font-family: Verdana, sans-serif;"></html></span><br />
<span style="font-family: Verdana, sans-serif;"> <table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh704wXrx4nqyZ_cjdNnN8DWHAe6QyF4htxAmF7nTDyvQeVl65S2biPQL8kUaWjIIw8eMMe9kPLzKoy2yUYod0qH4aFFT9l9e5wReQdL1Gtpsk51O0aLUm8fYiRSBZqLtKNH5UlY71Gw-Q/s1600/tableee.PNG" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="227" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh704wXrx4nqyZ_cjdNnN8DWHAe6QyF4htxAmF7nTDyvQeVl65S2biPQL8kUaWjIIw8eMMe9kPLzKoy2yUYod0qH4aFFT9l9e5wReQdL1Gtpsk51O0aLUm8fYiRSBZqLtKNH5UlY71Gw-Q/s400/tableee.PNG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><h2>
<span style="color: #0b5394;"><u><b>Making tables in HTML</b></u></span></h2>
</td></tr>
</tbody></table>
</span><br />
<span style="font-family: Verdana, sans-serif;"> </span></div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179472 72.770422600000018 33.9408292 73.415869600000008tag:blogger.com,1999:blog-7587796149281043589.post-55810385045461569182015-10-22T07:56:00.000-07:002015-10-22T07:56:56.541-07:00Making dynamic Facebook page in HTML (Lame Facebook page)<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">To make a simple Facebook page in HTML you must be well aware of usage of tables and forms in HTML. By using simple tags you can make simple login pages.</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">Here is the complete code in HTML to Facebook page !!!</span></div>
<span style="color: purple;"><b><u>CODE</u></b></span><br />
<span style="font-family: Verdana, sans-serif;"><html></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><body></span><br />
<span style="font-family: Verdana, sans-serif;"><caption> Facebook login page</caption><br></span><br />
<span style="font-family: Verdana, sans-serif;"><table border="0" BORDERCOLOR=blue style="width:100% "cellpadding="30"></span><br />
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"><th bgcolor="darkblue" align="left" > <FONT COLOR=WHITE FACE="Geneva, Arial" SIZE=6 >facebook</FONT> </th></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> <td bgcolor="darkblue" align="right"> <form name="facebook" method="post"></span><br />
<span style="font-family: Verdana, sans-serif;"> <input type="checkbox" name="check" value="facebook login" checked></span><br />
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"> <FONT COLOR=white FACE="Arial" align="left" Size=3></span><br />
<span style="font-family: Verdana, sans-serif;">keep me logged in &nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;</FONT></span><br />
<span style="font-family: Verdana, sans-serif;"> <FONT COLOR=white FACE="Arial" align="left" Size=3>forgot your password?<br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"> <input type="text" name=" " value="Bioinfo@gmail.com" size="20" maxlength="10"></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> <input type="password" name=" " value="nadiabaig" size="20" maxlength="10">&nbsp;&nbsp;<input type="submit" value="login"></td></span><br />
<span style="font-family: Verdana, sans-serif;"></tr> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><tr></span><br />
<span style="font-family: Verdana, sans-serif;"> <th bgcolor="lightblue" align="left"><FONT COLOR=DARKBLUE FACE="Geneva, Arial" SIZE=5 >Facebook helps you connect and share with<br>the people in your life.<br></span><br />
<span style="font-family: Verdana, sans-serif;"><img src="ffff.png" height="250" width="570"></span><br />
<span style="font-family: Verdana, sans-serif;"></th></span><br />
<span style="font-family: Verdana, sans-serif;"><th bgcolor="lightblue" align="left" ><FONT COLOR=DARKBLUE FACE="Geneva, Arial" SIZE=5 > Signup<br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=4 >It's free and anyone can join<hr><br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"><form name="signup" method="post"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 >First Name: &nbsp;&nbsp;&nbsp;&nbsp<input type="text" name="name" value=" " size="40"maxlength="15"><br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 >LastName:</span><br />
<span style="font-family: Verdana, sans-serif;">&nbsp;</span><span style="font-family: Verdana, sans-serif;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp<input type="text" name="lname" value=" " size="40"maxlength="15"><br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 >Your Email:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<input type="text" name="email" value=" " size="40"maxlength="15"><br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 >Re-enter Email:<input type="text" name="lname" value</span><span style="font-family: Verdana, sans-serif;">" " </span><span style="font-family: Verdana, sans-serif;">size="40"maxlength="15"><br></FONT></span><span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 >New Password:<input type="text" name="lname" value=" " size="40"maxlength="15"><br></FONT></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2 align="left" > I am:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<select name=sex></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="select sex">Select sex</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="M">Male</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="F">Female</option></span><br />
<span style="font-family: Verdana, sans-serif;"> </select><br></span><span style="font-family: Verdana, sans-serif;"> Birthday:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<select "name=month"></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="select month">Month</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">January</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="F">Febuary</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="M">March</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="A">April</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="Ma">May</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="Ju">June</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="Jul">July</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="Au">August</option></span><br />
<span style="font-family: Verdana, sans-serif;"></select></span><br />
<span style="font-family: Verdana, sans-serif;"><select "name=day"></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="select day">Day</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">01</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="k">02</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="l">03</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="m">04</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="n">05</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="o">06</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="p">07</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="q">08</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="r">09</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="s">10</option></span><br />
<span style="font-family: Verdana, sans-serif;"></select></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><select "name=year"></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="Year">Year</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="a">1990</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">1991</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">1992</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">1993</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">2011</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">2012</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">2013</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">2014</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">2015</option></span><br />
<span style="font-family: Verdana, sans-serif;"> <option value="J">1900</option></span><br />
<span style="font-family: Verdana, sans-serif;"> </select><br></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;why do I need to provide this?</a></FONT><br></span><br />
<span style="font-family: Verdana, sans-serif;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<input type="submit" value="Sign UP"button style="background-color:green"><hr><br></span><br />
<span style="font-family: Verdana, sans-serif;"><FONT COLOR=DARKBLUE FACE=" Arial" SIZE=2>&nbsp;&nbsp</FONT><FONT COLOR=BLACK FACE=" Arial" SIZE=2> create a page for a celebrity, fan or business<FONT><br></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"></td></span><br />
<span style="font-family: Verdana, sans-serif;"></table></span><br />
<span style="font-family: Verdana, sans-serif;"></body></span><br />
<span style="font-family: Verdana, sans-serif;"></html></span><br />
<span style="font-family: Verdana, sans-serif;"> </span><br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDYMLhwzxPIctwLiz7-10eFZnkZITpzRVbE6iJb2m6Oe3mP6Lnm6CAcx3EfEErbmYTa1q3sz26kIMUn7Pp-yD3N-uB8NyoM4UFKtlyt45B3bJ9qOzvxuDT4FlKPfIUlG4ecVoOuVAXkRA/s1600/lamebbb.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="259" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDYMLhwzxPIctwLiz7-10eFZnkZITpzRVbE6iJb2m6Oe3mP6Lnm6CAcx3EfEErbmYTa1q3sz26kIMUn7Pp-yD3N-uB8NyoM4UFKtlyt45B3bJ9qOzvxuDT4FlKPfIUlG4ecVoOuVAXkRA/s640/lamebbb.PNG" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><h2>
<span style="color: orange;">Static webpage Facebook</span></h2>
</td></tr>
</tbody></table>
<span style="color: purple;"><b><u><br /></u></b></span>
<br />
<span style="color: purple;"><b><u></u></b></span>
<span style="color: purple;"><b><u><br /></u></b></span></div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Gilgit35.920154 74.30801259999998435.817272499999994 74.146651099999985 36.0230355 74.469374099999982tag:blogger.com,1999:blog-7587796149281043589.post-79669557573755796872015-10-03T00:46:00.000-07:002015-10-03T00:46:12.602-07:00Variants of Basic PCR method, their principle, purpose and applications<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="color: orange; font-family: Verdana, sans-serif;"><br /></span></div>
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<b><span style="font-size: 14.0pt; line-height: 115%;"><span style="color: orange; font-family: Verdana, sans-serif;">PCR ( PolymeraseChain Reaction)</span></span></b></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="background: white; line-height: 115%;">The<span class="apple-converted-space"> </span><b>polymerase
chain reaction</b><span class="apple-converted-space"> </span>(<b>PCR</b>)
is a technology in<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Molecular_biology"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">molecular biology</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">used to<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA_replication"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">amplify</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">a single copy or a few copies of a piece of<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">DNA</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">across several orders of magnitude, generating thousands to millions of
copies of a particular<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA_sequence"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">DNA sequence</span></a><span style="background: white; line-height: 115%;">.<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="background: white; line-height: 115%;"><br /></span></span></div>
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<b><span style="background: white; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="color: magenta;">Principle of PCR</span><span style="color: #252525;"><o:p></o:p></span></span></span></b></div>
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<span style="font-family: Verdana, sans-serif;"><span style="background: white; line-height: 115%;">PCR uses the enzyme DNA polymerase
that directs the synthesis of DNA from deoxynucleotide substrates on a
single-stranded DNA template. DNA polymerase adds nucleotides to the 3` end of
a custom-designed oligonucleotide when it is annealed to a longer template DNA.
Thus, if a synthetic oligonucleotide is annealed to a single-stranded template
that contains a region complementary to the oligonucleotide, DNA polymerase can
use the oligonucleotide as a primer and elongate its 3` end to generate an
extended region of double stranded DNA.</span><b><span style="background: white; color: #252525; line-height: 115%;"><o:p></o:p></span></b></span></div>
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<span style="color: magenta;"><sup><span style="background: white; line-height: 115%;"><span style="font-family: Verdana, sans-serif; font-size: small;"> </span></span></sup><!--[endif]--></span></div>
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<b><span style="background: white; font-size: 14pt; line-height: 115%;"><span style="color: magenta; font-family: Verdana, sans-serif;">Applications and purpose</span></span></b><b><span style="font-size: 14.0pt; line-height: 115%;"><o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l1 level1 lfo1; text-indent: -.25in;">
</div>
<ul style="text-align: left;">
<li><span style="color: #252525; line-height: 115%; text-indent: -0.25in;"><span style="font-family: Verdana, sans-serif;"><span style="font-size: 14pt;">·</span><span style="font-size: 7pt; font-stretch: normal; line-height: normal;"> </span><span style="font-stretch: normal; line-height: normal;"> </span></span></span><span style="background: white; color: #252525; line-height: 115%; text-indent: -0.25in;"><span style="font-family: Verdana, sans-serif;">Selective DNA isolation</span></span></li>
<li><span style="font-family: Verdana, sans-serif;"><span style="color: #252525; line-height: 115%; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; color: #252525; line-height: 115%; text-indent: -0.25in;">Amplification and quantification of
DNA</span></span></li>
<li><span style="font-family: Verdana, sans-serif;"><span style="color: #252525; line-height: 115%; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; color: #252525; line-height: 115%; text-indent: -0.25in;">Disease Diagnosis</span></span></li>
<li><span style="font-family: Verdana, sans-serif;"><span style="color: #252525; line-height: 115%; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; color: #252525; line-height: 115%; text-indent: -0.25in;">Forensic Sciences</span></span></li>
</ul>
<!--[if !supportLists]--><br />
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<b><span style="background: white; font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Arial; mso-bidi-font-style: italic;"><span style="color: magenta; font-family: Verdana, sans-serif;">Variants of polymerase chain reaction</span><o:p></o:p></span></b></div>
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<b><span style="color: #f1c232; font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-color: white; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-size: 14pt; line-height: 115%;">1. </span><span style="background-attachment: initial; background-clip: initial; background-color: white; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">Multiplex-PCR</span></span></b><span class="apple-converted-space"><span style="background: white; font-size: 14.0pt; line-height: 115%; mso-bidi-font-family: Arial;"><b><span style="color: #f1c232; font-family: Verdana, sans-serif;"> </span></b><o:p></o:p></span></span></div>
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<span class="apple-converted-space"><span style="background: white; color: #252525; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Multiplex –PCR </span></span></span><span style="background: white; color: #252525; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">uses several
pairs of primers annealing to different target sequences. This permits the
simultaneous analysis of multiple targets in a single sample. For example, in
testing for genetic mutations, six or more amplifications might be combined. </span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
<div class="MsoNormal">
<b><span style="background: white; line-height: 115%;"><span style="color: #6aa84f; font-family: Verdana, sans-serif;">Principle</span><span style="color: #252525; font-size: 14pt;"><o:p></o:p></span></span></b></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="background: white; line-height: 115%;">This process<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA_replication" title="DNA replication"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">amplifies</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><a href="https://en.wikipedia.org/wiki/DNA" title="DNA"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">DNA</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">in samples using multiple<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Primer_(molecular_biology)" title="Primer (molecular biology)"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">primers</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">and a temperature-mediated<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA_polymerase" title="DNA polymerase"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">DNA
polymerase</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">in a<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Thermal_cycler" title="Thermal cycler"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">thermal
cycler</span></a><span style="background: white; line-height: 115%;">. The primer design for all primers pairs has to be
optimized so that all primer pairs can work at the same annealing temperature
during PCR.<span style="font-size: 14pt;"><o:p></o:p></span></span></span></div>
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<b><span style="background: white; line-height: 115%;"><span style="color: #6aa84f; font-family: Verdana, sans-serif;">Applications and purpose</span><span style="color: #252525; font-size: 14pt;"><o:p></o:p></span></span></b></div>
<div class="MsoListParagraphCxSpFirst" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; line-height: 115%;">Some of the<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Applications_of_PCR" title="Applications of PCR"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">applications</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">of multiplex PCR include<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;"> </span></span><span style="background: white; line-height: 115%;"> Pathogen
Identification<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; line-height: 115%;">High
Throughput SNP Genotyping<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; line-height: 115%;">Mutation Analysis<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; line-height: 115%;">Gene Deletion Analysis<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="background: white; line-height: 115%;">Template Quantitation<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; line-height: 115%;">Linkage Analysis<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; line-height: 115%;">RNA Detection<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--><span style="background: white; line-height: 115%;">Forensic Studies<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpLast" style="margin-left: 1.0in; mso-add-space: auto; mso-list: l2 level2 lfo6; tab-stops: list 1.0in; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><!--[endif]--></span><span style="background: white; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Diet Analysis</span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><b><span style="line-height: 115%;"><span style="color: #f1c232;">2.Real time PCR</span></span></b><span style="background: white; line-height: 115%;"> <o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="background: white; color: #252525; line-height: 115%;">A<span class="apple-converted-space"> </span></span><span style="background: white; line-height: 115%;">real-time polymerase chain reaction</span><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">is a<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Laboratory_technique" title="Laboratory technique"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">laboratory technique</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">of<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Molecular_biology" title="Molecular biology"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">molecular
biology</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">based on the </span><a href="https://en.wikipedia.org/wiki/Polymerase_chain_reaction" title="Polymerase chain reaction"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">polymerase chain reaction</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">(PCR). It monitors the amplification of a targeted<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA" title="DNA"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">DNA</span></a><span class="apple-converted-space"><span style="background: white; line-height: 115%;"> </span></span><span style="background: white; line-height: 115%;">molecule during the PCR, i.e. in real-time, and not at its end, as in
conventional PCR. Real-time PCR can be used quantitatively (</span><a href="https://en.wikipedia.org/w/index.php?title=Quantitative_real-time_PCR&action=edit&redlink=1" title="Quantitative real-time PCR (page does not exist)"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">Quantitative
real-time PCR</span></a><span style="background: white; line-height: 115%;">), semi-quantitatively (</span><a href="https://en.wikipedia.org/w/index.php?title=Semi_quantitative_real-time_PCR&action=edit&redlink=1" title="Semi quantitative real-time PCR (page does not exist)"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">Semi
quantitative real-time PCR</span></a><span style="background: white; line-height: 115%;">) or qualitatively (</span><a href="https://en.wikipedia.org/w/index.php?title=Qualitative_real-time_PCR&action=edit&redlink=1" title="Qualitative real-time PCR (page does not exist)"><span style="background: white; color: windowtext; mso-bidi-font-family: Arial;">Qualitative real-time PCR</span></a><span style="background: white; line-height: 115%;">).<o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="background: white; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> <o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<span style="font-family: Verdana, sans-serif;"><b><span style="color: #6aa84f;">Principle</span></b><b><o:p></o:p></b></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<span style="font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">Real-time PCR is carried out in a<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Thermal_cycler" title="Thermal cycler"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">thermal
cycler</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">with the
capacity to illuminate each sample with a beam of light of at least one
specified wavelength and detect the fluorescence emitted by the excited<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Fluorophore" title="Fluorophore"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">fluorophore</span></a><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">. The thermal cycler is also able to rapidly heat and
chill samples, thereby taking advantage of the physicochemical properties of
the<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Nucleic_acid" title="Nucleic acid"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">nucleic
acids</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">and<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/DNA_polymerase" title="DNA polymerase"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">DNA
polymerase</span></a><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">.</span><b><o:p></o:p></b></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<b><span style="font-family: Verdana, sans-serif;"><span style="color: #6aa84f;">Applications and purpose</span><span style="color: #252525;"><o:p></o:p></span></span></b></div>
<div class="MsoListParagraphCxSpFirst" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-add-space: auto; mso-list: l0 level1 lfo2; mso-margin-top-alt: auto; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">·<span style="font-stretch: normal; line-height: normal;"> </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">Real time PCR is applied to rapidly detect<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Nucleic_acid"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">nucleic acids</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">that are diagnostic of, for
example,<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Infectious_diseases"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">infectious
diseases</span></a><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">,<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Cancer"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">cancer</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">and genetic abnormalities<o:p></o:p></span></span></div>
<div class="MsoListParagraphCxSpLast" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-add-space: auto; mso-list: l0 level1 lfo2; mso-margin-top-alt: auto; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">·<span style="font-stretch: normal; line-height: normal;"> </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">Real time PCR is also used by microbiologists working
in the fields of food safety, food spoilage and fermentation and for the
microbial risk assessment of water quality (drinking and recreational waters)
and in public health protection</span></span><b><span style="font-size: 14.0pt; mso-bidi-font-family: Arial; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></b></div>
<h3 style="background: white; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: 0in; margin-top: .05in; mso-list: l0 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span class="mw-headline"><span style="font-family: Symbol; font-size: 14pt; font-weight: normal;">·<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal;">
</span></span></span><!--[endif]--><span class="mw-headline"><span style="font-family: Calibri, sans-serif; font-size: 14pt; font-weight: normal;">Detection of
phytopathogens<o:p></o:p></span></span></h3>
<h3 style="background: white; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: .5in; margin-right: 0in; margin-top: .05in; mso-list: l0 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span class="mw-headline"><span style="font-family: Symbol; font-size: 14pt; font-weight: normal;">·<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal;">
</span></span></span><!--[endif]--><span class="mw-headline"><span style="font-family: Calibri, sans-serif; font-size: 14pt; font-weight: normal;">Detection of
genetically modified organisms<o:p></o:p></span></span></h3>
<h3 style="background: white; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: 0in; margin-right: 0in; margin-top: .05in;">
<span style="font-family: Verdana, sans-serif; font-size: small;"><span style="color: #f1c232;">3. </span><i><span style="color: #f1c232;">Hot-start PCR</span><span style="color: #252525;"><o:p></o:p></span></i></span></h3>
<h3 style="background: white; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: 0in; margin-right: 0in; margin-top: .05in;">
<span style="font-family: Verdana, sans-serif; font-size: small;"><span style="color: #252525; font-weight: normal;">It is a technique performed manually by heating the
reaction components to the DNA melting temperature (e.g. 95 °C) before
adding the polymerase. In this way, non-specific amplification at lower
temperatures is prevented. Alternatively, specialized reagents inhibit the
polymerase's activity at ambient temperature, either by the binding of </span><span style="font-weight: normal;">an </span><a href="https://en.wikipedia.org/wiki/Antibody" title="Antibody"><span style="color: windowtext; font-weight: normal; text-decoration: none;">antibody</span></a><span style="color: #252525; font-weight: normal;">, or by the presence of covalently bound inhibitors
that only dissociate after a high-temperature activation step.
'Hot-start/cold-finish PCR' is achieved with new hybrid polymerases that are
inactive at ambient temperature and are only activated at elevated
temperatures.<o:p></o:p></span></span></h3>
<h2 style="background: white; margin: 0.05in 0in 0.0001pt; text-align: left;">
<span style="color: #38761d; font-family: Verdana, sans-serif; font-size: small;">Principle </span></h2>
<h3 style="background: white; margin-bottom: .0001pt; margin-bottom: 0in; margin-left: 0in; margin-right: 0in; margin-top: .05in;">
<span style="font-size: small;"><span style="color: #252525;"><span style="font-family: Verdana, sans-serif;"> </span></span><span style="font-family: Verdana, sans-serif; font-weight: normal;">Hot start PCR works by using </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-family: Verdana, sans-serif; font-weight: normal;">a more sensitive technique than standard PCR that
allows amplification of low-abundance targets and single-copy genes while
reducing PCR background problems.</span></span></h3>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<span style="font-family: Verdana, sans-serif;"><span style="color: #f1c232;"><b>4. </b><b><i><span style="text-decoration: none;">Assembly PCR</span></i></b></span><b><i><o:p></o:p></i></b></span></div>
<div class="MsoNormal" style="background: white; margin-bottom: 1.2pt;">
<span style="font-family: Verdana, sans-serif;"><i style="line-height: 16.8pt;">Assembly
PCR is </i><span style="color: #252525;"><span style="line-height: 16.8pt;"> (also known as </span></span><i style="color: #252525; line-height: 16.8pt;">Polymerase
Cycling Assembly</i><span style="color: #252525;"><span style="line-height: 16.8pt;"> or </span></span><i style="color: #252525; line-height: 16.8pt;">PCA</i><span style="color: #252525;"><span style="line-height: 16.8pt;">) is the synthesis of long DNA
structures by performing PCR on a pool of long </span><span style="line-height: 22.4px;">oligonucleotide s</span><span style="line-height: 16.8pt;"> with short overlapping segments, to assemble two or more pieces of DNA into one piece. It
involves an initial PCR with primers that have an overlap and a second PCR
using the products as the template that generates the final full-length
product. This technique may substitute fo</span></span><span style="line-height: 16.8pt;">r </span><a href="https://en.wikipedia.org/wiki/DNA_ligase" style="line-height: 16.8pt;" title="DNA ligase"><span style="color: windowtext; text-decoration: none;">ligation</span></a><span style="color: #252525; line-height: 16.8pt;">-based assembly. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<b><span style="font-family: Verdana, sans-serif;"><span style="color: #6aa84f;">Principle </span><span style="color: #252525;"><o:p></o:p></span></span></b></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<span style="font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: #333333;">Single-stranded oligos or a mix of
single- and double-stranded DNA is used to produce longer genes of up to
several thousand base pairs.<span class="apple-converted-space"> </span></span><span style="color: #252525;"><o:p></o:p></span></span></div>
<div class="MsoNormal" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-margin-top-alt: auto;">
<b><span style="font-family: Verdana, sans-serif;"><span style="color: #38761d;">Applications and purpose</span><span style="color: #252525;"><o:p></o:p></span></span></b></div>
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<ul style="text-align: left;">
<li><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">Used in novel gene
synthesis</span></li>
<li><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">Cloning double
stranded DNA into plasmid vector</span></li>
</ul>
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<span style="font-family: Verdana, sans-serif;"><b style="color: #6aa84f;">5</b><span style="color: #f1c232;">.
<b><span style="text-decoration: none;">Allele-specific PCR</span></b><b>:</b></span><span style="color: #252525;"> <o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;">A diagnostic or cloning technique
based on single-nucleotide variations (SNVs not to be confused with ( <a href="https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism" title="Single-nucleotide polymorphism"><span style="color: windowtext; text-decoration: none; text-underline: none;">SNPs</span></a>) (single-base
differences in a patient). It requires prior knowledge of a DNA sequence,
including differences between <a href="https://en.wikipedia.org/wiki/Allele" title="Allele"><span style="color: windowtext; text-decoration: none;">alleles</span></a>, and uses primers whose 3' ends encompass the SNV (base pair buffer
around SNV usually incorporated.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;"><b><span style="color: #6aa84f;">Principle</span></b><b><o:p></o:p></b></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="color: #252525;">Based on a single
nucleotide polymorphism (SNP, s). PCR
amplification under stringent conditions is much less efficient in the presence
of a mismatch between template and primer, so successful amplification with an
SNP-specific primer signals presence of the specific SNP in a sequence</span><span style="color: #252525;">.</span><span style="color: #252525;"> <o:p></o:p></span></span></div>
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<b><span style="font-family: Verdana, sans-serif;"><span style="color: #6aa84f;">Applications and purpose</span><span style="color: #252525;"><o:p></o:p></span></span></b></div>
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<ul style="text-align: left;">
<li><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">Clinical HIV
genotyping</span></li>
<li><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·<span style="font-stretch: normal; line-height: normal;">
</span></span><span style="color: #252525; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">SNP genotyping</span></li>
</ul>
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<span style="font-family: Verdana, sans-serif;"><b><span style="color: #f1c232;">6. <i>Suicide PCR</i></span></b><span style="color: #252525;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;">It is typically used in <a href="https://en.wikipedia.org/wiki/Paleogenetics" title="Paleogenetics"><span style="color: windowtext; text-decoration: none; text-underline: none;">paleogenetics</span></a> or
other studies where avoiding false positives and ensuring the specificity of
the amplified fragment is the highest priority. It was originally described in
a study to verify the presence of the microbe <a href="https://en.wikipedia.org/wiki/Yersinia_pestis" title="Yersinia pestis"><span style="color: windowtext; text-decoration: none; text-underline: none;">Yersinia
pestis</span></a> in dental samples obtained from 14th Century graves of
people supposedly killed by plague during the medieval <a href="https://en.wikipedia.org/wiki/Black_Death" title="Black Death"><span style="color: windowtext; text-decoration: none;">Black Death</span></a> epidemic<span style="color: #252525;">.<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><b><span style="color: #6aa84f;">Principle</span></b><span style="color: #252525;"><o:p></o:p></span></span></div>
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<span style="color: #252525;"><span style="font-family: Verdana, sans-serif;">The method
prescribes the use of any primer combination only once in a PCR (hence the term
"suicide"), which should never have been used in any positive control
PCR reaction, and the primers should always target a genomic region never
amplified before in the lab using this or any other set of primers. This
ensures that no contaminating DNA from previous PCR reactions is present in the
lab, which could otherwise generate false positives.<sup><o:p></o:p></sup></span></span></div>
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<b><span style="font-family: Verdana, sans-serif;"><span style="color: #6aa84f;">Applications and purpose</span><span style="color: #252525;"><o:p></o:p></span></span></b></div>
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</div>
<ul style="text-align: left;">
<li><span style="font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·</span><span style="font-family: Verdana, sans-serif; font-stretch: normal; line-height: normal; text-indent: -0.25in;">
</span><span style="font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">Used in the field of
palaeomicrobiology</span></li>
<li><span style="font-family: Verdana, sans-serif; line-height: 115%; text-indent: -0.25in;">· </span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Diagnosis of Rickettsioses</span></li>
</ul>
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<b><span style="font-family: Verdana, sans-serif;"><span style="color: #f1c232;">7.Reverse transcription PCR (RT PCR)</span><o:p></o:p></span></b></div>
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<span style="font-family: Verdana, sans-serif;"><span style="color: #0e232b;">In reverse transcription polymerase chain reaction
(RT-PCR), first a RNA strand (template) is reverse transcribed into its
complementary DNA copy using reverse transcriptase, and subsequently cDNA is
amplified using PCR.Various types of<span class="apple-converted-space"> </span><em>Reverse
transcriptase</em><span class="apple-converted-space"><i> </i></span>enzyme,
isolated from<span class="apple-converted-space"> </span><em>Avian
myeloblastosis virus (AMV),Moloney murine leukemia virus (MMLV</em><span class="apple-converted-space"><i> </i></span>or<span class="apple-converted-space"> </span><em>MuLV)</em><span class="apple-converted-space"><i> </i></span>are
generally used to produce a DNA copy from RNA template. Random primers, an
oligo (dT) primer or sequence-specific prim</span><span style="color: #0e232b;">ers are used to amplify cDNA.</span></span></div>
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<b><span style="font-family: Verdana, sans-serif;"><span style="color: #6aa84f;">Principle</span><span style="color: #0e232b;"><o:p></o:p></span></span></b></div>
<div class="MsoNormal" style="background: white; line-height: 17.25pt; margin-bottom: 15.0pt; vertical-align: baseline;">
<span style="font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">In RT-PCR, the<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/RNA" title="RNA"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">RNA</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">template is first converted into a<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Complementary_DNA" title="Complementary DNA"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">complementary
DNA</span></a><span class="apple-converted-space"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> </span></span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">(cDNA)
using a<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Reverse_transcriptase" title="Reverse transcriptase"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">reverse transcriptase</span></a><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;">. The cDNA
is then used as a template for exponential amplification using PCR</span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: #252525;">.</span><b><span style="color: #0e232b;"><o:p></o:p></span></b></span></div>
<div class="MsoListParagraphCxSpFirst" style="background: white; line-height: 16.8pt; margin-bottom: 1.2pt; mso-add-space: auto; mso-list: l3 level1 lfo5; mso-margin-top-alt: auto; tab-stops: list .5in; text-indent: -.25in;">
</div>
<ul style="text-align: left;">
<li><span style="font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·</span><span style="font-family: Verdana, sans-serif; font-stretch: normal; line-height: normal; text-indent: -0.25in;"> </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">RT-PCR can also be very useful in the insertion of
eukaryotic genes into protectorates</span></li>
<li><span style="font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">·</span><span style="font-family: Verdana, sans-serif; font-stretch: normal; line-height: normal; text-indent: -0.25in;"> </span><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">RT-PCR can be used to diagnose genetic disease such as<span class="apple-converted-space"> </span></span><a href="https://en.wikipedia.org/wiki/Lesch%E2%80%93Nyhan_syndrome" style="font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;" title="Lesch–Nyhan syndrome"><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; color: windowtext;">Lesch–Nyhan syndrome</span></a><span style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; font-family: Verdana, sans-serif; line-height: 16.8pt; text-indent: -0.25in;">.</span></li>
<li><span style="background-color: transparent; font-family: Verdana, sans-serif; line-height: 115%;"> Cancer Detection</span></li>
</ul>
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Gilgit35.920154 74.30801259999998435.817272499999994 74.146651099999985 36.0230355 74.469374099999982tag:blogger.com,1999:blog-7587796149281043589.post-77499041421663759862015-07-30T05:41:00.021-07:002015-07-30T05:41:29.360-07:00Basic pascal programing language codes<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-GB"><span style="color: #cc0000; font-family: Verdana, sans-serif;"><b>Write a program that reads two integers and then displays <o:p></o:p></b></span></span></div>
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<span style="color: #cc0000; font-family: Verdana, sans-serif;"><span class="apple-converted-space"><span lang="EN-GB"><b> a) Their product<o:p></o:p></b></span></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<span style="color: #cc0000;"><b><span style="font-family: Verdana, sans-serif;"><span class="apple-converted-space"><span lang="EN-GB"><span style="font-stretch: normal;"> b) </span></span></span></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Their quotient when the first is divided by the second</span></b></span></div>
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<br /></div>
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<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">program
product(input, output);<o:p></o:p></span></span></span></div>
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<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">uses
crt;<o:p></o:p></span></span></span></div>
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<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">var
a,b,c,d:integer;<o:p></o:p></span></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">begin<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(‘Enter an integer’);<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln(a);<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(‘Enter an integer’);<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln(b);<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">c=a*b;<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(c)<br />
d:=a div b;<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(d)<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln;<br />
<span style="background-attachment: initial; background-clip: initial; background-color: #ffffee; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"> end.</span></span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="background-attachment: initial; background-clip: initial; background-color: #ffffee; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"><br /></span></span></span></div>
</div>
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<b><span style="font-size: 14pt; line-height: 115%;"> </span></b></div>
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<span style="line-height: 115%;"><span style="color: magenta; font-family: Verdana, sans-serif;"><b>Write a program that
uses nested loop to find prime numbers from 2 to 50.</b></span><span style="font-size: 14pt; font-weight: bold;"><o:p></o:p></span></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"><br /></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">Program
nestedprime;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">uses crt;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">var<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">i,j:=integer;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">begin<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"> for j:=2 to 50 do<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">begin<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"> for j:=2 to i do<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"> if (i mod j)=0 then<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"> break;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">if(j=1) then<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">writeln(i ,
‘is prime’);<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">end;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">end.<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"><br /></span></div>
</div>
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<b><span style="color: #231f20; font-size: 14.0pt; mso-bidi-font-family: CenturyOldstBT;"><br /></span></b></div>
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<b><span style="color: #0b5394; font-family: Verdana, sans-serif;">Write a program to calculate the population of a city at the end
of each year from<o:p></o:p></span></b></div>
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<b><span style="color: #0b5394; font-family: Verdana, sans-serif;">1990 to 2000. Use the following assumptions:<o:p></o:p></span></b></div>
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<b><span style="color: #0b5394; font-family: Verdana, sans-serif;">a. Initial population at the end of 1989 = 5 million<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="color: #0b5394; font-family: Verdana, sans-serif;">b. Yearly death ratio = 3%<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="color: #0b5394; font-family: Verdana, sans-serif;">c. Yearly birth ratio = 7%</span><span style="color: #231f20; font-size: 14pt;"><o:p></o:p></span></b></div>
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<br /></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">program
population;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">uses crt;<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;">var<o:p></o:p></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"> P,B,D:=integer;<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">P :=
5000000.0 ;<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">begin<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">for i := 1990 to 2000 do <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">begin<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">B:= 0.07 * P;<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;"> D:= 0.03; <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">P:= P + B -
D; <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">Writeln(‘Details
of total population each year is’);<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">writeln(i:10,
P:20:2); <o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">end;<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 14.0pt; line-height: 115%;">end.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<br />
<div class="MsoNormal">
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-56113493506434918272015-06-27T01:44:00.000-07:002015-07-30T05:30:02.150-07:00primary and secondary structure prediction for APRT (human) protein sequence<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: 12.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">APRT(human)<o:p></o:p></span></b></div>
<div class="MsoNormal">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-font-weight: bold; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman"; mso-font-kerning: 18.0pt;">RecName: Full=Adenine phosphoribosyltransferase<o:p></o:p></span></div>
<div class="MsoNormal">
<b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman"; mso-font-kerning: 18.0pt;">Fasta format<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">>gi|114074|sp|P07741.2|APT_HUMAN
RecName: Full=Adenine phosphoribosyltransferase; Short=APRT<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Primary
structure prediction<o:p></o:p></span></b></div>
<h1 style="margin-left: .5in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">1.<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal; font-weight: normal;">
</span></span><!--[endif]--><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">ProtParam<o:p></o:p></span></h1>
<h1>
<span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; font-weight: normal; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-font-weight: bold; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Physico-chemical parameters of a protein sequence (amino-acid and atomic
compositions, isoelectric point, extinction coefficient, etc.<o:p></o:p></span></h1>
<pre><span style="font-size: 14.0pt;"> </span></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Number of amino acids:</span></b> 180</pre>
<pre><o:p> </o:p></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Molecular weight</span></b><b><span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">:</span></b> 19607.7</pre>
<pre><o:p> </o:p></pre>
<form>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Amino acid composition</span></b><b><span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">:</span></b><span style="font-size: 14.0pt;"> <o:p></o:p></span></pre>
<pre>
Ala (A) 16 8.9%</pre>
<pre>Arg (R) 12 6.7%</pre>
<pre>Asn (N) 1 0.6%</pre>
<pre>Asp (D) 9 5.0%</pre>
<pre>Cys (C) 3 1.7%</pre>
<pre>Gln (Q) 7 3.9%</pre>
<pre>Glu (E) 13 7.2%</pre>
<pre>Gly (G) 17 9.4%</pre>
<pre>His (H) 2 1.1%</pre>
<pre>Ile (I) 7 3.9%</pre>
<pre>Leu (L) 29 16.1%</pre>
<pre>Lys (K) 8 4.4%</pre>
<pre>Met (M) 2 1.1%</pre>
<pre>Phe (F) 8 4.4%</pre>
<pre>Pro (P) 11 6.1%</pre>
<pre>Ser (S) 11 6.1%</pre>
<pre>Thr (T) 6 3.3%</pre>
<pre>Trp (W) 1 0.6%</pre>
<pre>Tyr (Y) 4 2.2%</pre>
<pre>Val (V) 13 7.2%</pre>
<pre>Pyl (O) 0 0.0%</pre>
<pre>Sec (U) 0 0.0%</pre>
<pre><o:p> </o:p></pre>
<pre> (B) 0 0.0%</pre>
<pre> (Z) 0 0.0%</pre>
<pre> (X) 0 0.0%</pre>
</form>
<pre><o:p> </o:p></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></b></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Total number of negatively charged residues (Asp + Glu):</span></b> 22</pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Total number of positively charged residues (Arg + Lys):</span></b> 20</pre>
<pre><o:p> </o:p></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Atomic composition:</span></b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></pre>
<pre><o:p> </o:p></pre>
<pre>Carbon C 885</pre>
<pre>Hydrogen H 1423</pre>
<pre>Nitrogen N 237</pre>
<pre>Oxygen O 254</pre>
<pre>Sulfur S 5</pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Extinction coefficients:</span></b><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></b></pre>
<pre><o:p> </o:p></pre>
<pre>Extinction coefficients are in units of M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.</pre>
<pre><o:p> </o:p></pre>
<pre>Ext. coefficient 11585</pre>
<pre>Abs 0.1% (=1 g/l) 0.591, assuming all pairs of Cys residues form cystines</pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Ext. coefficient 11460</pre>
<pre>Abs 0.1% (=1 g/l) 0.584, assuming all Cys residues are reduced</pre>
<pre><o:p> </o:p></pre>
<pre><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Instability index:</span></b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></pre>
<pre><o:p> </o:p></pre>
<pre>The instability index (II) is computed to be 39.29</pre>
<pre>This classifies the protein as stable.</pre>
<pre>*****************************************************************************</pre>
<pre style="margin-left: .5in; mso-list: l0 level1 lfo1; text-indent: -.25in;"><!--[if !supportLists]--><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">2.<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal;"> </span></span><!--[endif]--><b><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Compute pI/Mw</span></b><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></pre>
<pre><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Compute the theoretical isoelectric point (pI) and molecular weight (Mw) from a UniProt Knowledgebase entry or for a user sequence<o:p></o:p></span></pre>
<pre>Theoretical pI/Mw: 5.75 / 19607.77<a href="https://www.blogger.com/null" name="_GoBack"></a><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></pre>
<pre><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></pre>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">3.<span style="font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;">
</span></span></b><!--[endif]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">ScanSitepI/Mw<o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpLast">
<span style="font-size: 12.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Compute the
theoretical pI and Mw, and multiple phosphorylation states<o:p></o:p></span></div>
<pre><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-font-kerning: 18.0pt; mso-hansi-theme-font: minor-latin;"> </span></b></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-font-kerning: 18.0pt; mso-hansi-theme-font: minor-latin;"> </span></b></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-font-kerning: 18.0pt; mso-hansi-theme-font: minor-latin;"> </span></b></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-font-kerning: 18.0pt; mso-hansi-theme-font: minor-latin;"> </span></b></pre>
<pre><b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-font-kerning: 18.0pt; mso-hansi-theme-font: minor-latin;">Protein: APRT (human)</span></b><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><o:p></o:p></span></pre>
<table border="1" cellpadding="0" class="MsoNormalTable" style="border: outset 1.5pt; mso-cellspacing: 1.5pt; mso-yfti-tbllook: 1184;">
<tbody>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">#
Phosphates<o:p></o:p></span></b></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Molecular
Weight<o:p></o:p></span></b></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Isoelectric
Point<o:p></o:p></span></b></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="color: blue; font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">0</span></b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19607.5431<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">5.78<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">1<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19685.5071<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">5.49<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">2<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19763.4711<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">5.29<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">3<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19841.4351<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">5.12<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19919.3991<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4.99<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">5<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">19997.3631<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4.87<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">6<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">20075.3271<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4.77<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">7<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">20153.2911<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4.68<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">8<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">20231.2551<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt;">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">4.59<o:p></o:p></span></div>
</td>
</tr>
</tbody></table>
<pre><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt;"> </span></pre>
<pre><o:p> </o:p></pre>
<pre>Theoretical pI/Mw: 5.75 / 19607.77</pre>
<pre>*****************************************************************************</pre>
<pre style="margin-left: .5in; mso-list: l0 level1 lfo1; text-indent: -.25in;"><!--[if !supportLists]--><b><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">4.<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></span></b><!--[endif]--><b><span style="font-family: "Calibri","sans-serif"; font-size: 16.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">ProtScale<o:p></o:p></span></b></pre>
<pre><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Amino acid scale representation (Hydrophobicity, other conformational parameters<o:p></o:p></span></pre>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">SEQUENCE LENGTH:
179<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Using the scale </span><a href="http://web.expasy.org/protscale/pscale/Hphob.Doolittle.html"><b><span style="color: windowtext; font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Hphob. / Kyte&
Doolittle</span></b></a><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">,
the individual values for the 20 amino acids are: <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Ala: 1.800
Arg: -4.500 Asn: -3.500 Asp: -3.500
Cys: 2.500 Gln: -3.500
<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Glu:
-3.500 Gly: -0.400 His: -3.200
Ile: 4.500 Leu:
3.800 Lys: -3.900 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Met: 1.900
Phe: 2.800 Pro: -1.600
Ser: -0.800 Thr: -0.700 Trp: -0.900
<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Tyr:
-1.300 Val: 4.200
: -3.500 : -3.500 : -0.490
<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Weights for
window positions 1,..,9, using <b>linear weight variation model</b>:<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> 1
2 3 4
5 6 7
8 9 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">1.00 1.00
1.00 1.00 1.00
1.00 1.00 1.00
1.00 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">edge center edge<o:p></o:p></span></div>
<pre><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt;"> </span></pre>
<pre><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt;">
</span></pre>
<pre>
</pre>
<div class="MsoListParagraph">
<br /></div>
<div align="center" class="MsoNormal" style="text-align: center;">
<b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Secondary structure prediction<o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpFirst" style="margin-left: .75in; mso-add-space: auto; mso-list: l1 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">1.<span style="font-size: 7pt; font-stretch: normal; font-weight: normal; line-height: normal;">
</span></span></b><!--[endif]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">CFSSP<o:p></o:p></span></b></div>
<div class="MsoListParagraphCxSpLast">
<span style="font-size: 12.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Chou
&amp; Fasman Secondary Structure Prediction Server<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Name of the
sequence is <i>gi|114074|sp|P07741.2|APT_HUMAN RecName: Full=Adenine
phosphoribosyltransferase; Short=APRT. </i><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Sequence consists
of 180 amino acids.<o:p></o:p></span></div>
<div class="MsoNormal">
<b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Target
Sequence: </span></b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">MADSELQLVE
QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY IAGLDSRGFL <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">FGPSLAQELG
LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG QRVVVVDDLL ATGGTMNAAC <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ELLGRLQAEV
LECVSLVELT SLKGREKLAP VPFFSLLQYE <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Secondary
Structure: </span></b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> * * * * * <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Query
1
MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDY 60 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Helix
1 HHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 60 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Sheet
1 EEEEEEEE EEEEEE 60 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Turns
1 T TTTT
60 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> * * * * * <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Query
61
IAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPG 120 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Helix
61 HHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHH 120 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Sheet
61 EEEEEEEE EEE 120 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Turns
61 TT T
TTT TT T TT
120<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> * * * * * <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Query
121 QRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Helix
121 HHHHHHHHHH
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH 180<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Sheet
121 EEEEEEEEEE
EEEEEEEEEEEEEEEEEEEEE
EEEEEEEE 180 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Turns
121 T TTTT 180 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Total
Residues: H: 132 E: 64 T: 21
<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Percent: H: 73.3 E: 35.6
T: 11.7 <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoListParagraphCxSpFirst" style="margin-left: .75in; mso-add-space: auto; mso-list: l1 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">2.<span style="font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><!--[endif]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">GOR</span></b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><o:p></o:p></span></div>
<div class="MsoListParagraphCxSpLast">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 115%;">Garnier et al, 1996<o:p></o:p></span></div>
<pre><code> 10 20 30 40 50 60 70<o:p></o:p></code></pre>
<pre><code> | | | | | | |<o:p></o:p></code></pre>
<pre><code>MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL<o:p></o:p></code></pre>
<pre><code><span style="color: orange;">ccccc</span><span style="color: blue;">hhhhhhhh</span><span style="color: orange;">cccccccccc</span><span style="color: red;">eeee</span><span style="color: orange;">ccccccccc</span><span style="color: blue;">hhhhhhhhhhhhhhhh</span><span style="color: orange;">ccccc</span><span style="color: red;">eeeee</span><span style="color: orange;">cccccccc</span><o:p></o:p></code></pre>
<pre><code>FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC<o:p></o:p></code></pre>
<pre><code><span style="color: orange;">ccc</span><span style="color: blue;">hhhhhh</span><span style="color: orange;">cc</span><span style="color: blue;">hhhhhh</span><span style="color: orange;">cccccccc</span><span style="color: red;">ee</span><span style="color: orange;">c</span><span style="color: red;">eee</span><span style="color: orange;">c</span><span style="color: blue;">hhhhhhhhhhhhhhh</span><span style="color: orange;">cccc</span><span style="color: red;">eeeeeeeee</span><span style="color: orange;">cccc</span><span style="color: blue;">hhhhhh</span><o:p></o:p></code></pre>
<pre><code>ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE<o:p></o:p></code></pre>
<pre><code><span style="color: blue;">Hhhhhhhhhhhhhhhhhhhh</span><span style="color: orange;">cccccccccccccccccc</span><span style="color: red;">ee<o:p></o:p></span></code></pre>
<pre><code> </code></pre>
<pre>Sequence length : 180</pre>
<pre>GOR4 :</pre>
<pre> Alpha helix (<span style="color: blue;">Hh</span>) : 77 is 42.78%</pre>
<pre>3<sub>10 </sub> helix (<span style="color: blue;">Gg</span>) : 0 is 0.00%</pre>
<pre> Pi helix (<span style="color: blue;">Ii</span>) : 0 is 0.00%</pre>
<pre> Beta bridge (<span style="color: red;">Bb</span>) : 0 is 0.00%</pre>
<pre> Extended strand (<span style="color: red;">Ee</span>) : 25 is 13.89%</pre>
<pre> Beta turn (<span style="color: green;">Tt</span>) : 0 is 0.00%</pre>
<pre> Bend region (<span style="color: orange;">Ss</span>) : 0 is 0.00%</pre>
<pre> Random coil (<span style="color: orange;">Cc</span>) : 78 is 43.33%</pre>
<pre>Ambiguous states (?) : 0 is 0.00%</pre>
<pre> Other states : 0 is 0.00%</pre>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal" style="margin-left: .5in;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 115%;">************************************************************************<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpFirst" style="margin-left: .75in; mso-add-space: auto; mso-list: l1 level1 lfo2; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "Times New Roman","serif"; font-size: 16.0pt; line-height: 115%; mso-fareast-font-family: "Times New Roman";">3.<span style="font-family: 'Times New Roman'; font-size: 7pt; font-stretch: normal; line-height: normal;"> </span></span><!--[endif]--><b><span style="font-size: 16.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Jpred</span></b><span style="font-family: "Times New Roman","serif"; font-size: 16.0pt; line-height: 115%;"><o:p></o:p></span></div>
<div class="MsoListParagraphCxSpLast">
<span style="font-size: 12.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">A consensus
method for protein secondary structure prediction at University of Dundee<o:p></o:p></span></div>
<table border="0" cellpadding="0" class="MsoNormalTable">
<tbody>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt; width: 78.25pt;" width="104">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">PDB
<o:p></o:p></span></b></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 74.7pt;" width="100">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Chain
<o:p></o:p></span></b></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 170.8pt;" width="228">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Description
<o:p></o:p></span></b></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 74.65pt;" width="100">
<div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Blast
E-value <o:p></o:p></span></b></div>
</td>
</tr>
<tr>
<td style="padding: .75pt .75pt .75pt .75pt; width: 78.25pt;" width="104">
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<a href="http://www.ebi.ac.uk/pdbsum/1zn9" target="PDBsum" title="PDBsum link"><span style="color: windowtext; font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman"; text-decoration: none; text-underline: none;">1zn9</span></a><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 74.7pt;" width="100">
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">B<o:p></o:p></span></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 170.8pt;" width="228">
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">Adenine phosphoribosyltransferase<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
</td>
<td style="padding: .75pt .75pt .75pt .75pt; width: 74.65pt;" width="100">
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-fareast-font-family: "Times New Roman";">2e-98<o:p></o:p></span></div>
</td>
</tr>
</tbody></table>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; line-height: 115%;">******************************************************************************<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoListParagraph" style="margin: 0in 0in 0.0001pt 0.75in; text-indent: -0.25in;">
<!--[if !supportLists]--><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">4.<span style="font-size: 7pt; font-stretch: normal;">
</span></span><!--[endif]--><b><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">PSIpred</span></b><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin: 0in 0in 0.0001pt 0.25in;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Various
protein structure prediction methods at Bloomsbury Centre for Bioinformatics<o:p></o:p></span></div>
<div class="MsoNormal" style="margin: 0in 0in 0.0001pt 0.25in;">
<br /></div>
<div class="MsoNormal" style="margin: 0in 0in 0.0001pt 0.25in;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">***************************************************************************<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpFirst" style="margin: 0in 0in 0.0001pt 0.75in; text-indent: -0.25in;">
<!--[if !supportLists]--><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">5.<span style="font-size: 7pt; font-stretch: normal;">
</span></span><!--[endif]--><b><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">SOPMA</span></b><span style="font-size: 16.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><o:p></o:p></span></div>
<div class="MsoListParagraphCxSpMiddle" style="margin-bottom: 0.0001pt;">
<span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Geourjon
and Delage, 1995<o:p></o:p></span></div>
<div class="MsoListParagraphCxSpLast" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> 10 20 30 40 50 60 70<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> | | | | | | |<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFL<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhhhhhhhhh</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">t</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ccccccccc</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">eeee</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ccccccccc</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhhhhhhhhhhhh</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ttt</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cc</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">eeeeee</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ccc</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">tt</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">c</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">e</span><span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">FGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAAC<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">e</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cc</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhh</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">t</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cc</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">eeeee</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">tt</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cccccccc</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">e</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhhh</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">t</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">c</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhhhhh</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cc</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">tt</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">c</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">eeeeee</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhh</span><span style="color: green; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">tt</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">cc</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhh</span><span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hhhhhhhhhhhhhhhhhhhhh</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">ccccccccccc</span><span style="color: red; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">eeeee</span><span style="color: blue; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">hh</span><span style="color: orange; font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">c</span><span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Sequence
length : 180<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">SOPMA :<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Alpha helix (<span style="color: blue;">Hh</span>)
: 83 is 46.11%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">3<sub>10
</sub> helix (<span style="color: blue;">Gg</span>)
: 0 is 0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Pi helix (<span style="color: blue;">Ii</span>)
: 0 is 0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Beta bridge (<span style="color: red;">Bb</span>) : 0 is
0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Extended strand (<span style="color: red;">Ee</span>)
: 29 is 16.11%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Beta turn (<span style="color: green;">Tt</span>)
: 14 is 7.78%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Bend region (<span style="color: orange;">Ss</span>)
: 0 is 0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Random coil (<span style="color: orange;">Cc</span>)
: 54 is 30.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">Ambiguous
states (?) : 0 is
0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Other states :
0 is 0.00%<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 12.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: "Times New Roman";">Parameters
:<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Window width :
17<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Similarity threshold : 8<o:p></o:p></span></div>
<br />
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";"> Number of states :
4<o:p></o:p></span></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-76360466338258380712015-06-09T14:45:00.000-07:002015-06-09T14:45:16.240-07:00Java program to make simple calculator including its GUI<div dir="ltr" style="text-align: left;" trbidi="on">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicjoHASww-ebaHNwBv_VOXI98CL-DUH8m7rA5UUcbzwbuUs8qHr7azsLd050ocL_58bIKk1Iv2iLe-CGO6pZd9JTAJgKH8oC3uY2SKm5q8Un7fEQYkeXRFp-euEvHhgHcsDqeaoPs4sBU/s1600/download+%25281%2529.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="223" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicjoHASww-ebaHNwBv_VOXI98CL-DUH8m7rA5UUcbzwbuUs8qHr7azsLd050ocL_58bIKk1Iv2iLe-CGO6pZd9JTAJgKH8oC3uY2SKm5q8Un7fEQYkeXRFp-euEvHhgHcsDqeaoPs4sBU/s320/download+%25281%2529.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Calculator in JAVA</td></tr>
</tbody></table>
<br />
<br />
<br />
<span style="font-family: Verdana, sans-serif;">import javax.swing.JFrame;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import javax.swing.JButton;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import javax.swing.JLabel;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import javax.swing.JPanel;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import javax.swing.JTextField;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.BorderLayout;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.FlowLayout;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.GridLayout;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.Color;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.event.ActionListener;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">import java.awt.event.ActionEvent;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">public class calculator extends JFrame implements ActionListener</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">{</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> public static final int WIDTH=300;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> public static final int HEIGTH=200;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> public JTextField name;</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> public static void main(String[] args)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> calculator gui= new calculator();</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> gui.setVisible(true);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> public calculator()</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> super("Calculator");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> setSize(WIDTH,HEIGTH);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> setLayout(new BorderLayout());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JPanel panel1=new JPanel();</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> panel1.setLayout(new GridLayout(1,1));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JTextField name= new JTextField();</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> panel1.add(name);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> add(panel1, BorderLayout.NORTH);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JPanel buttonpanel= new JPanel();</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.setBackground(Color.LIGHT_GRAY);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.setLayout(new GridLayout(4,4));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton onebutton= new JButton("1");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> onebutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(onebutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton twobutton= new JButton("2");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> twobutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(twobutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton threebutton= new JButton("3");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> threebutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(threebutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton plusbutton= new JButton("+");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> plusbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(plusbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton fourbutton= new JButton("4");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> fourbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(fourbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton fivebutton= new JButton("5");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> fivebutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(fivebutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton sixbutton= new JButton("6");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> sixbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(sixbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton minusbutton= new JButton("-");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> minusbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(minusbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton sevenbutton= new JButton("7");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> sevenbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(sevenbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton eightbutton= new JButton("8");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> eightbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(eightbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton ninebutton= new JButton("9");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> ninebutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(ninebutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton multibutton= new JButton("*");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> multibutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(multibutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton zerobutton= new JButton("0");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> zerobutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(zerobutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton pointbutton= new JButton(".");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> pointbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(pointbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton equalbutton= new JButton("=");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> equalbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(equalbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton dividebutton= new JButton("/");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> dividebutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> buttonpanel.add(dividebutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> JButton cbutton= new JButton("C");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> cbutton.addActionListener(this);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> panel1.add(cbutton);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> add(buttonpanel, BorderLayout.CENTER);</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">public void actionPerformed (ActionEvent e)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> String text= e.getActionCommand();</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> if(text.equals("1"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">{</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("1");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">}</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("2"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("2");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("3"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("3");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("4"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> { </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("4");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">} </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("5"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("5");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("6"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("6"); </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("7"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("7");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("8"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("8"); </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("9"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("9");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("0"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText("0");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("."))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText(".");</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("+"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> result=result + stringToDouble(name.getText());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText(Double.toString(result));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("-"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> result=result - stringToDouble(name.getText());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText(Double.toString(result));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("*"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> result=result * stringToDouble(name.getText());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText(Double.toString(result));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> else if(text.equals("/"))</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> result=result / stringToDouble(name.getText());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> name.setText(Double.toString(result));</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> private static double stringToDouble(String stringObject)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> {</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> return Double.parseDouble(stringObject.trim());</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> }</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">}</span></div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179472 72.770422600000018 33.9408292 73.415869600000008tag:blogger.com,1999:blog-7587796149281043589.post-36278918470218266922015-06-09T14:37:00.003-07:002015-06-09T14:37:54.533-07:00Bubble sort in c++<div dir="ltr" style="text-align: left;" trbidi="on">
<pre class="a-c-x-Ha a-c-Ma-td-Ib" style="-webkit-user-select: text; background-color: white; font-size: 14px; white-space: pre-wrap; word-wrap: break-word;"><span style="font-family: Verdana, sans-serif;">#include <iostream>
#include <conio.h>
using namespace std;
int main()
{
int bubble[10];
int temp;
int i;
int j;
cout<<" enter the elements in the array "<<endl;
for (i=0; i<10; i++)
{
cout<<" Element "<<i<<" : ";
cin>>bubble[i];
}
/// bubble sorting
for (i=0; i<10; i++)
{
for (j=0; j<i; j++)
{
if(bubble[j]>bubble[i])
///int temp to do the swapping and store value
{
int temp=bubble[j];
bubble[j]=bubble[i];
bubble[i]=temp;
}
}
}
cout<<" The sorted array is as follows : "<<endl;
for (i=0; i<10; i++)
{
cout<<" \n Element "<<i<<" : "<<bubble[i];
}
getch ();
return 0;
}
</span></pre>
<div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbLJ2iVVIQdam8Ss8KNP83LbkWeEm3W0cubQyFRyoUJAdMTLThSf58JakPTZJ5STwcDItM7T1WweSp1ldFycC9-slAzbOPn-JACxt0hyphenhyphenn174Z_YJXERsvUu2CWh3dJcm25PeLJfaPf-ww/s1600/82dcf7083edabaa90e0ca88ed849854d.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="102" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbLJ2iVVIQdam8Ss8KNP83LbkWeEm3W0cubQyFRyoUJAdMTLThSf58JakPTZJ5STwcDItM7T1WweSp1ldFycC9-slAzbOPn-JACxt0hyphenhyphenn174Z_YJXERsvUu2CWh3dJcm25PeLJfaPf-ww/s320/82dcf7083edabaa90e0ca88ed849854d.jpg" width="320" /></a></div>
<div>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-42850785598776455612015-06-06T11:22:00.001-07:002015-06-06T11:22:16.100-07:00Pascal program to find prime numbers (2 to 50)<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">program
product(input, output);<o:p></o:p></span></span></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">uses
crt;<o:p></o:p></span></span></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span class="apple-converted-space"><span lang="EN-GB"><span style="font-family: Verdana, sans-serif;">var
a,b,c,d:integer;<o:p></o:p></span></span></span></div>
<br />
<div style="border-bottom: dotted windowtext 3.0pt; border: none; mso-element: para-border-div; padding: 0in 0in 1.0pt 0in;">
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">begin<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(‘Enter an integer’);<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln(a);<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(‘Enter an integer’);<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln(b);<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">c=a*b;<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(c)<br />
d:=a div b;<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">writeln(d)<o:p></o:p></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">readln;<br />
</span><span style="background-attachment: initial; background-clip: initial; background-color: #ffffee; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial;"><span style="font-family: Verdana, sans-serif;"> end.</span><span style="font-size: 14pt;"><o:p></o:p></span></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="background: #FFFFEE;"><br /></span></span></div>
<div class="MsoNormal" style="border: none; mso-border-bottom-alt: dotted windowtext 3.0pt; mso-padding-alt: 0in 0in 1.0pt 0in; padding: 0in;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="background: #FFFFEE;"><br /></span></span></div>
</div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-2866414245333850192015-06-06T11:14:00.003-07:002015-06-06T11:17:55.327-07:00Difference between C, JAVA and Pascal<div dir="ltr" style="text-align: left;" trbidi="on">
<div align="center" class="MsoNormal" style="text-align: center;">
<br /></div>
<div class="MsoNormal">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; line-height: 115%; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Java<o:p></o:p></span></b></div>
<div class="MsoNormal" style="text-align: left;">
<span style="line-height: 115%;"><span style="font-size: 14pt;">j</span><span style="font-family: Verdana, sans-serif;">ava</span></span><span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"> is a
general-purpose </span><span style="color: windowtext; line-height: 115%;">computer programming
language</span><span style="line-height: 115%;"> that is </span><span style="color: windowtext; line-height: 115%;">concurrent</span><span style="line-height: 115%;">, class based</span><span style="line-height: 115%;">, object oriented</span></span><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">, and specifically designed to have
as few implementation dependencies as possible. One design goal of Java is
portability, which means that programs written for the Java platform must run
similarly on any combination of hardware and operating system with adequate
run time support.</span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
<div class="MsoNormal">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; line-height: 115%; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Pascal<o:p></o:p></span></b></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">Pascal</span><span style="line-height: 115%;"> is a
historically influential </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">imperative</span><span style="line-height: 115%;"> and </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">procedural </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">programming language</span><span style="line-height: 115%;">, designed in 1968–1969 and published
in 1970 by </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">Niklaus Wirth</span><span style="line-height: 115%;"> as a small and efficient language
intended to encourage good programming practices using </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">structured
programming</span><span style="line-height: 115%;"> and </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">data structuring</span></span><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">.</span><span style="font-size: 12pt;"><o:p></o:p></span></span></div>
<div class="MsoNormal">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; line-height: 115%; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">C<o:p></o:p></span></b></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">C</span><span style="line-height: 115%;"> is a
general-purpose, </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">imperative</span><span style="line-height: 115%;"> computer </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">programming language</span><span style="line-height: 115%;">. It supports </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">structured
programming</span><span style="line-height: 115%;">, </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">lexical variable scope</span><span style="line-height: 115%;"> and </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">recursion</span><span style="line-height: 115%;">, while a </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">static type system</span><span style="line-height: 115%;"> prevents many unintended operations.
By design, C provides constructs that map efficiently to typical </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">machine instructions</span><span style="line-height: 115%;">, and therefore it has found lasting
use in applications that had formerly been coded in </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">assembly language</span><span style="line-height: 115%;">, including </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">operating systems</span><span style="line-height: 115%;">, as well as various </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">application software</span><span style="line-height: 115%;"> for computers ranging from </span><span style="color: windowtext; line-height: 115%; text-decoration: none;">supercomputers</span><span style="line-height: 115%;"> to </span></span><span style="color: windowtext; line-height: 115%; text-decoration: none;"><span style="font-family: Verdana, sans-serif;">embedded system</span><span style="font-size: 14pt;">s</span></span><span style="font-size: 14.0pt; line-height: 115%;"><a href="http://./">.</a><o:p></o:p></span></div>
<div class="MsoNormal">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; line-height: 115%; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Difference<o:p></o:p></span></b></div>
<table border="1" cellpadding="0" cellspacing="0" class="MsoTableGrid" style="border-collapse: collapse; border: none; mso-border-alt: solid windowtext .5pt; mso-padding-alt: 0in 5.4pt 0in 5.4pt; mso-yfti-tbllook: 1184; width: 644px;">
<tbody>
<tr style="height: 7.95pt; mso-yfti-firstrow: yes; mso-yfti-irow: 0;">
<td style="border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Description<o:p></o:p></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">C<o:p></o:p></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Java<o:p></o:p></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-family: "Cambria","serif"; font-size: 16.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;">Pascal<o:p></o:p></span></b></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 1;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></span></b><!--[endif]--><b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Comments<o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">/* comment */<b><o:p></o:p></b></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-font-weight: bold; mso-bidi-theme-font: minor-latin;">// is used for
comments<o:p></o:p></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">{ comment }<b><o:p></o:p></b></span></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 2;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></span></b><!--[endif]--><b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">for loop<o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-font-weight: bold; mso-bidi-theme-font: minor-latin;">For (int
1=10;i<=10;i++)<b><o:p></o:p></b></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-font-weight: bold; mso-bidi-theme-font: minor-latin;">For (int
1=10;i<=10;i++)<o:p></o:p></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">for i := 1 to 10 do <em><span style="font-family: "Calibri","sans-serif"; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">statement</span></em><b><o:p></o:p></b></span></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 3;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></span></b><!--[endif]--><b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">operators<o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">% <br />
/</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">% <br />
/</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">mod <br />
div</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 4;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 18.6666660308838px; font-stretch: normal;"> </span><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></b><!--[endif]--><b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">Declaration<o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Integer
declaration)<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">inti,j,k;<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Array
declaration)<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">sInt A[10];<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Integer
declaration)<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">inti,j,k;<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Array
declaration)<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">int[] A = new int[10]; <br />
<b>or</b>int A[] = new int[10];<b><o:p></o:p></b></span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Integer
declaration)</span></b><span style="font-size: 14.0pt;"> i,j,k:integer<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b><span style="font-size: 14.0pt;">(Array
declaration)<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">A:array[0..9] of integer<b><o:p></o:p></b></span></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 5;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 18.6666660308838px; font-stretch: normal;"> </span><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></b><!--[endif]--><b><span style="font-size: 14.0pt;">Functions</span></b><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">char a (int b) <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">{ <br />
...<br />
return 'X';<br />
}</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">char a (int b)<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;"> { <br />
...<br />
return 'X';<br />
}</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">function a(b:integer):char <br />
begin<br />
...<br />
a:='X'<br />
end;</span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
</tr>
<tr style="height: 7.95pt; mso-yfti-irow: 6; mso-yfti-lastrow: yes;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 132.15pt;" valign="top" width="176"><div class="MsoListParagraph" style="margin-bottom: 0.0001pt; text-indent: -0.25in;">
<b><span style="font-size: 14.0pt; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="font-size: 7pt; font-stretch: normal; font-weight: normal;"> </span></span></b><!--[endif]--><b><span style="font-size: 14.0pt;">Reverse
for loop<o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">for (int i=10; i>0; i--) <br />
<em><span style="font-family: "Calibri","sans-serif"; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">statement</span></em></span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 117.15pt;" valign="top" width="156"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">for (int i=10; i>0; i--) <br />
<em><span style="font-family: "Calibri","sans-serif"; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">statement</span></em></span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 7.95pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0in 5.4pt 0in 5.4pt; width: 116.25pt;" valign="top" width="155"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-size: 14.0pt;">for i := 10 downto 1 do <br />
<em><span style="font-family: "Calibri","sans-serif"; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">statement</span></em></span><b><span style="font-family: "Cambria","serif"; font-size: 14.0pt; mso-ascii-theme-font: major-latin; mso-hansi-theme-font: major-latin;"><o:p></o:p></span></b></div>
</td>
</tr>
</tbody></table>
<br /></div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-16446868057249366292015-06-05T11:46:00.000-07:002015-06-05T11:55:14.178-07:00TicTacToe in C++<div dir="ltr" style="text-align: left;" trbidi="on">
//Nadia baig<br />
<br />
#include <iostream><br />
#include<conio.h><br />
<br />
using namespace std;<br />
<br />
<br />
void tictac(char board[][3]);<br />
char Winner(char board[][3]);<br />
<br />
int main(){<br />
char board[3][3]={{'*','*','*'},{'*','*','*'},{'*','*','*'}};<br />
bool win = false;<br />
bool in_row = false;<br />
bool in_col = false;<br />
int i;<br />
int j;<br />
<br />
<br />
<br />
<br />
// run a loop:<br />
while (!win) {<br />
<br />
tictac(board); /// displays board<br />
cout << "Player 1's turn:";<br />
cout << "enter row to insert value\n";<br />
cin >>i;<br />
cout << "enter coloumn\n";<br />
cin >> j;<br />
// check if move is valid<br />
bool valid = false;<br />
while (!valid)<br />
{<br />
//check if the move is in range.<br />
if(!(i <= 3 && i >= 1 && j<= 3 && j >= 1)){<br />
cout << "Error: value inserted greater than size of matrix\n";<br />
// ask again (error: row in column not within range)<br />
cout << "enter row:?\n";<br />
cin >> i;<br />
cout << "enter column?\n";<br />
cin >> j;<br />
}<br />
else if(board[i-1][j-1] != '*')<br />
{<br />
cout << "Error: Position is occupied already\n";<br />
cout << "enter row:?\n";<br />
cin >> i;<br />
cout << "enter/ column?\n";<br />
cin >> j;<br />
}else {<br />
valid = true;<br />
}<br />
<br />
<br />
}<br />
board[i-1][j-1] = 'X';<br />
tictac(board);<br />
// Check if someone won or if there is a tie<br />
Winner(board);<br />
// Ask player two to chose a location (row, column)<br />
cout << "Player 2's turn:";<br />
<br />
cout << "enter row:?\n";<br />
cin >> i;<br />
cout << "enter column?\n";<br />
cin >> j;<br />
// check if move is valid<br />
<br />
<br />
valid = false;<br />
while (!valid)<br />
{<br />
//check if the move is within range.<br />
if(!(i <= 3 && i >= 1 && j <= 3 && j >= 1)){<br />
cout << "Error: value entered is not in range.\n";<br />
<br />
cout << "enter row:?\n";<br />
cin >> i;<br />
cout << "enter column?\n";<br />
cin >> j;<br />
}<br />
else if(board[i-1][j-1] != '*')<br />
{<br />
cout << "Error: position is already occupied.\n";<br />
cout << "enter row:?\n";<br />
cin >> i;<br />
cout << "enter column?\n";<br />
cin >> j;<br />
}else<br />
{<br />
valid = true;<br />
}<br />
board[i-1][j-1] = 'O';<br />
}<br />
tictac(board);<br />
// Check if someone won or if there is a tie<br />
Winner(board);<br />
<br />
}<br />
<br />
<br />
<br />
return 0;<br />
}<br />
char Winner(char board[][3]){<br />
char winner = 'T';<br />
<br />
// horizontal:<br />
for (int i = 0; i < 3; i++)<br />
if (board[i][0] == board[i][1] && board[i][1] == board[i][2])<br />
winner = board[i][0];<br />
<br />
// vertical:<br />
for (int i = 0; i < 3; i++)<br />
if (board[0][i] == board[1][i] && board[1][i] == board[2][i])<br />
winner = board[0][1];<br />
<br />
// diagnol:<br />
if ((board[0][0] == board[1][1] && board[1][1] == board[2][2]) ||<br />
(board[0][2] == board[1][1] && board[1][1] == board[2][0]))<br />
winner = board[1][1];<br />
<br />
// result:<br />
switch (winner) {<br />
case 'T': cout << " TIE"; break;<br />
case 'X': cout << "PLAYER 1 WON! congratulations"; break;<br />
case 'O': cout << "PLAYER 2 WON! congratulations";break;<br />
default : cout << "NEXT PLAYER'S TURN...>";<br />
}<br />
return winner;<br />
}<br />
void tictac(char board[][3])<br />
{<br />
<br />
cout << " 1 2 3" << endl;<br />
cout << " +---+---+---+" << endl;<br />
<br />
cout << " 1" << " | " << board[0][0] << " | " << board[0][1] << " | " << board[0][2] << " | " << endl;<br />
cout << " +---+---+---+" << endl;<br />
<br />
cout << " 2" << " | " << board[1][0] << " | " << board[1][1] << " | " << board[1][2] << " | " << endl;<br />
cout << " +---+---+---+" << endl;<br />
<br />
cout << " 3" << " | " << board[2][0] << " | " << board[2][1] << " | " << board[2][2] << " | " << endl;<br />
cout << " +---+---+---+" << endl;<br />
<br />
}<br />
<div>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-85767825534226985992015-06-05T11:43:00.001-07:002015-06-05T11:43:39.671-07:00Itertool module in python<div dir="ltr" style="text-align: left;" trbidi="on">
<span style="color: red; font-family: Verdana, sans-serif;">#Nadia baig</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">import</span> itertools</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">seq=<span style="color: purple;">input</span>(<span style="color: #38761d;">"Enter sequence to apply itertool functions\n"</span>)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(seq)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="color: red; font-family: Verdana, sans-serif;"># 1Applying product rule</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">def</span> <span style="color: blue;">pro</span>(seq,repeat=2):</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;"> return</span> (<span style="color: purple;">list </span>(itertools.product(seq, repeat=2)))</span><br />
<span style="font-family: Verdana, sans-serif;">p=pro(seq,repeat=2)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="color: red; font-family: Verdana, sans-serif;">#2Applying permutation</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">def</span><span style="color: blue;"> per</span>(seq,rep=2):</span><br />
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;"> return</span> (<span style="color: purple;"> list</span>(itertools.permutations(seq, 2)))</span><br />
<span style="font-family: Verdana, sans-serif;">q=per(seq,2)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="color: red; font-family: Verdana, sans-serif;">#3Applying combination</span><br />
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">def</span> <span style="color: blue;">com</span>(seq,rep=2):</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> return</span> (<span style="color: purple;">list</span>(itertools.combinations(seq,2)))</span><br />
<span style="font-family: Verdana, sans-serif;">c=com(seq,2)</span><br />
<span style="color: red; font-family: Verdana, sans-serif;"><br /></span>
<span style="color: red; font-family: Verdana, sans-serif;">#4 Applying combinations with replacement</span><br />
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">def </span><span style="color: blue;">comr</span>(seq,rep=2):</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> return </span>(<span style="color: purple;">list</span>(itertools.combinations_with_replacement(seq,2)))</span><br />
<span style="font-family: Verdana, sans-serif;">d=comr(seq,2)</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="color: red; font-family: Verdana, sans-serif;">#Menu</span><br />
<span style="font-family: Verdana, sans-serif;">choice=<span style="color: #6aa84f;">"please select any choice to perform following operations\n to apply product rule press 1\n press 2 to perform permutatino\n press 3 to apply combination\n press 4 to apply combinations with replacement\n"</span></span><br />
<span style="font-family: Verdana, sans-serif;">val=<span style="color: purple;">input</span>(choice)</span><br />
<span style="font-family: Verdana, sans-serif;">num=<span style="color: purple;">int</span>(val)</span><br />
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">for </span>choice <span style="color: orange;">in </span>val:</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;">if </span>(num==1):</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: purple;">print</span>(p)</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> elif</span> (num==2):</span><br />
<span style="font-family: Verdana, sans-serif;"> print(q)</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;">elif</span> (num==3):</span><br />
<span style="font-family: Verdana, sans-serif;"> print(c)</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;">elif </span>(num==4):</span><br />
<span style="font-family: Verdana, sans-serif;"> print(d)</span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;">else:</span></span><br />
<span style="font-family: Verdana, sans-serif;"> <span style="color: purple;"> print</span>("error")</span><br />
<div>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Gilgit35.9201595 74.30797510000002135.8172785 74.146613600000023 36.023040499999993 74.46933660000002tag:blogger.com,1999:blog-7587796149281043589.post-13894389135490850502015-06-03T12:22:00.001-07:002015-06-03T12:22:35.953-07:00Cryptarithmetic problem <div dir="ltr" style="text-align: left;" trbidi="on">
<span style="font-family: Verdana, sans-serif;"><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">Verbal arithmetic</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, also known as </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">alphametics</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">cryptarithmetic</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">crypt-arithmetic</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">cryptarithm</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;"> or </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">word addition</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, is a type of </span><span style="background-color: white; color: #252525;">mathematical game</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;"> consisting of a mathematical </span><span style="background-color: white; color: #252525;">equation </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">among unknown </span><span style="background-color: white; color: #252525;">numbers</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">, whose </span><span style="background-color: white; color: #252525;">digits </span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">are represented by </span><span style="background-color: white; color: #252525;">letters</span><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;">. The goal is to identify the value of each letter. The name can be extended to puzzles that use non-alphabetic symbols instead of letters.</span></span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">following java code implements cryptarithmetic problem.</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> T O O</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">+ T O O</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> T O O</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> ----------------</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> G O O D</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> ----------------</span><br />
<span style="background-color: white; color: #252525; font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">T=1, O=2, G=3, D=4</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="background-color: white; color: #252525; font-size: 14px; line-height: 22.3999996185303px;"><br /></span>
<span style="color: #252525;"><span style="font-size: 14px; line-height: 22.3999996185303px;">import java.util.Scanner;</span></span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">public class cryptoarithmatic</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">{</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> public static void main(String args[])</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> for (int T = 0; T <= 9; T++)</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> for (int O= 0; O <= 9; O++)</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> for (int G= 0; G <= 9; G++)</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> for (int D= 0; D <= 9; D++)</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> </span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> if ((T != O) && (T != G) && (T != D) && (O != G) && (O!= D) && (G != D)){</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> int too = T* 100 + O * 10 + O, good = G * 1000 + O * 100 + O* 10 + D;</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> if (good == 4 *too)</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> {</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println( " T = " +T);</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println(" O= " +O);</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println("O = " +O);</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println("G = " +G);</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println("D = " +D);</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> </span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println("TOO = "+ too );</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> System.out.println( "GOOD = " +good );</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;"> }</span></span><br />
<span style="font-family: Verdana, sans-serif;"><span style="color: #252525;"><span style="background-color: white; font-size: 14px; line-height: 22.3999996185303px;"></span></span><br /></span>
<span style="color: #252525;"><span style="font-family: Verdana, sans-serif; font-size: 14px; line-height: 22.3999996185303px;">}</span></span><br />
<div>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-42348244556370566802015-05-29T12:55:00.000-07:002015-05-29T12:55:49.841-07:00Parsing large files having different contigs( contigs contain details about genes)<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">Following python source code counts the total number of contigs present in a file and extracts number of genes, Complementary DNA strand, and other information. This program will run on files downloaded from NCBI.</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="color: red; font-family: Verdana, sans-serif;">#Nadia Baig</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">fr=<span style="color: purple;">open</span>(<span style="color: #38761d;">"C:\\Users\\XYZ\\Desktop\\chromosome.gbk,r"</span>) <span style="color: red;">#Path and file name</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">a=fr.read()</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">b=a.split(<span style="color: #6aa84f;">"//\n"</span>) <span style="color: red;">#split the whole file on //</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">length=<span style="color: purple;">len</span>(b)#counting length</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">i=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">genes=[]</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">for </span>base <span style="color: orange;">in</span> b:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> a=base.split(<span style="color: #6aa84f;">"\n"</span>)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;"> for</span> bb <span style="color: orange;">in</span> a:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> if </span>bb.startswith(<span style="color: #6aa84f;">" gene </span>") :</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> i=i+1</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> genes.append(i)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(genes) <span style="color: red;"># printing information about contigs having genes</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">total=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">j=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">while</span> j<<span style="color: purple;">len</span>(genes):</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> if</span> genes[j]==0:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> total=total+1 <span style="color: red;"> #counting contigs having no genes</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> j=j+1</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">Tgene=<span style="color: purple;">sum</span>(genes)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">"total number of genes present in file"</span>,Tgene) <span style="color: red;"> #total number of genes present in contig</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">"total number of contigs having no genes are"</span>,total)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="color: red; font-family: Verdana, sans-serif;"># printing those genes which have an attached cds or mRNA</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="color: red; font-family: Verdana, sans-serif;">#Having attached CDS</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">cds=[]</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">i=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">for</span> CDS <span style="color: orange;">in</span> b:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> c=CDS.split(<span style="color: #6aa84f;">"\n"</span>)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> for</span> cds1 <span style="color: orange;">in</span> c:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> if</span> cds1.startswith(<span style="color: #6aa84f;">" CDS " </span>):</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> i=i+1</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> cds.append(i)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> i=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">"details of CDS"</span>) </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(cds) <span style="color: red;"> #showing list of genes having attached cds</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">nad=<span style="color: purple;">sum</span>(cds) <span style="color: red;"> #TOtal number of cds</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">'total number of attached cds</span>',nad)</span></div>
<div style="text-align: left;">
<span style="color: red; font-family: Verdana, sans-serif;">#genes having attached mRNA</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">mrna=[]</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">i=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: orange;">for</span> CDS <span style="color: orange;">in</span> b:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> c=CDS.split(<span style="color: #93c47d;">"\n"</span>)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> for</span> cds1 <span style="color: orange;">in </span>c:</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> <span style="color: orange;"> if</span> cds1.startswith(<span style="color: #6aa84f;">" mRNA "</span>):</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> i=i+1</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> mrna.append(i)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> i=0</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">"details of genes having attached mRNA"</span>) </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(mrna)<span style="color: red;"> # list of total number of attached mrna,s in each contig</span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">msum=sum(mrna) <span style="color: red;">#Total number of attached mrna,s in all contigs</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="color: purple;">print</span>(<span style="color: #6aa84f;">'total number of attached mrnas</span>',msum)</span></div>
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<span style="font-family: Verdana, sans-serif;"> </span></div>
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<span style="font-family: Verdana, sans-serif;"> </span></div>
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<span style="font-family: Verdana, sans-serif;"> </span></div>
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Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0tag:blogger.com,1999:blog-7587796149281043589.post-40089737779872563852015-04-25T13:35:00.000-07:002015-04-25T13:35:57.723-07:00Implementing Local alignment in c++<div dir="ltr" style="text-align: left;" trbidi="on">
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<span class="ManText"><span style="font-family: Verdana, sans-serif;">A local alignment aligns a substring of the query sequence to a substring of the target sequence. The substrings may be all of one or both sequences; if all of both are included then the local alignment is also global. A local alignment is defined by maximizing the alignment score<span style="color: black;">,</span> so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score. For example, consider this global protein alignment:</span></span></div>
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<span style="font-family: Courier;"><b> </b></span><span class="ManCode" style="font-family: Courier;"><b> <span style="color: #cc0000;">Query WSEQVDNCEA</span></b></span></div>
<span class="ManCode" style="font-family: Courier;"><b><span style="color: #cc0000;"> ||||+|||</span></b></span><span class="ManCode" style="font-family: Courier;"><b><span style="color: #cc0000;"> </span></b></span><br />
<span class="ManCode" style="font-family: Courier;"><b><span style="color: #cc0000;"> Target KSEQVENCEN</span></b></span><br />
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<span class="ManCode"><b><span style="color: #7f6000; font-family: Verdana, sans-serif;">C++ CODE</span></b></span><br />
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<span class="ManCode"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="font-family: Verdana, sans-serif;">#include <string></span></div>
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<span style="font-family: Verdana, sans-serif;">#include <iostream></span></div>
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<span style="font-family: Verdana, sans-serif;">#include<conio.h></span></div>
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<span style="font-family: Verdana, sans-serif;">using namespace std;</span></div>
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<span style="font-family: Verdana, sans-serif;"> int main()</span></div>
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<span style="font-family: Verdana, sans-serif;">{</span></div>
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<span class="Apple-tab-span" style="white-space: pre;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>string base1;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>string base2;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>int gap=0;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>int match=+2;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>int mismatch=1;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>int d,h,v;</span></div>
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<span class="Apple-tab-span" style="white-space: pre;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
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<span class="Apple-tab-span" style="white-space: pre;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<" enter 1st string"<<endl;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cin>>base1;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<"enter your second string"<<endl;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cin>>base2;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<"Second string you entered is; "<<base1<<endl;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<"Second string you entered is; "<<base2<<endl;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int len1=base1.length()+1; </span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int len2=base2.length()+1;</span></div>
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<span style="font-family: Verdana, sans-serif;">/////dynamic array initializing</span></div>
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<span style="font-family: Verdana, sans-serif;"> ////int arr1[len1][len2] gives compiler error so to overcome it we make dynamic array</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int** arr1= new int*[len1];</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int i=0;i<len1;i++)</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i]=new int[len2];</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> ////filling of rows and columns</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[0][0]=0;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> ////row filling</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int j=1;j<len2;j++)</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[0][j]=0;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> //// column filling</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for(int i=1;i<len1;i++)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i][0]=0;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> //// string comparison ////</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int i=1;i<len1;i++)</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int j=1;j<len2;j++)</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> if (base1[i-1]==base2[j-1])</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> d=arr1[i-1][j-1]+match;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> //// for mismatch</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> else</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> d=arr1[i-1][j-1]+mismatch;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> v=arr1[i-1][j]+gap;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> h=arr1[i][j-1]+gap;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> if (d>v&&d>h&&d>0)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i][j]=d;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> else if (h>d && h>v&&h>0)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i][j]=h;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> else if (v>d && v>h&&v>0)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i][j]=v;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> else if (d==v ||d==h|| v==h||d==0)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> arr1[i][j]=d;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> //printing of the array</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for(int i=0;i<len1;i++)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>{</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int j=1;j<len2;j++)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<arr1[i][j]<<"\t";</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>}</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> cout<<endl;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>}</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> //// code for backtracking</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int r;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int c;</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int a=len1; //// row</span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> int b=len2; //// coloumn</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> char* arr2= new char[len1];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> char* arr3= new char[len2];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> for (int r=0;r<len1;r--)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span class="Apple-tab-span" style="white-space: pre;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>for (int a=len1;a>=len1;a--)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>for (int j=len2;j>=0;j--)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>if (arr1[a][b]==d)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>{</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>arr2[r]=base1[a];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> arr3[c]=base2[b];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> a--;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> b--;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> r++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> c++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>else if (arr1[a][b]==v)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>arr2[r]='-';</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>arr3[c]=base2[b];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>b--;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>r++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>c++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span> else if (arr1[a][b]==h)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>{</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>arr2[r]=base1[a];</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>arr3[c]='-';</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>a--;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>r++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>c++;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>}</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
<div style="text-align: left;">
<span class="Apple-tab-span" style="white-space: pre;"><span style="font-family: Verdana, sans-serif;"> </span></span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> for (int r=len1;r>=len1;r--)<span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"> {</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>for (int c=len2;c>=0;c--)</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>{</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;">cout<<arr2[r]<<"\t";</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span>cout<<arr3[c]<<"\t";</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> </span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>getch ();</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>return 0;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span>cout<<endl;</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<div style="text-align: left;">
<span style="font-family: Verdana, sans-serif;"><span class="Apple-tab-span" style="white-space: pre;"> </span> }</span></div>
<span style="color: #7f6000; font-family: Verdana, sans-serif;"><b><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span></b></span><br />
<span class="ManCode"><b><span style="color: #7f6000; font-family: Verdana, sans-serif;"></span></b></span><br />
<span style="color: #7f6000; font-family: Verdana, sans-serif;"><b><span class="Apple-tab-span" style="white-space: pre;"> </span> <span class="Apple-tab-span" style="white-space: pre;"> </span></b></span><br />
<div>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/11735236698241939560noreply@blogger.com0Islamabad, Pakistan33.7293882 73.09314610000001333.5179692 72.770422600000018 33.9408072 73.415869600000008