Basic software tools in bioinformatics

Useful Bioinformatics tools are open source and are easily available on net. Some of the commonly used tools ,links and their introduction is given below.
EMBOSS : This software is used for sequence alignment, protein structure prediction, motif finding, nucleotide sequence pattern analysis
Source: http://emboss.sourceforge.net
FASTA and SSEARCH : Fasta is used for the similarity search against protein database and SSEARCH is used a local alignment search tool and helpful to find best alignment score.
Source: http://www.ebi.ac.uk/Tools/sss/
BLAST : It is a basic local alignment search tool.
Source: http://www.ebi.ac.uk/Tools/sss/
GenePattern : It is a gene analysis platform that provides access to tools for gene expression and analysis. 
Source: http://www.broadinstitute.org/cancer/software/genepattern/
Biocarta : Brings the pathways and tools to observe how genes interact in dynamic graphical model.
Source: http://www.biocarta.com/
ClustalW2 : It is a multiple sequence alignment tool for DNA and protein sequences.It returns the best match scores by alignment of DNA sequences.
Source: http://www.ebi.ac.uk/Tools/msa/clustalw2/
Multiple Sequence Alignment tools: tools of MSA include MUSCLE, Clustal Omega, Kalign, MAFFT,T-Coffee,Mview. All of these alignment tools generally use two or more than two sequnces for the alignment to find out the best matches, evolutionary relationships amoung the sequences obtained from different organisms.
Source: http://www.ebi.ac.uk/Tools/msa/
MEME : It is a motif finding tool.This software tooks input in the form of DNA or protein sequence and give result in the form of possible motifs.
Source: http://meme.ebi.edu.au/meme/
ORF finder : This software tool is used to find the possible open reading frames of a given sequence.
Source: http://www.ncbi.nlm.nih.gov/projects/gorf/
LALIGN : Used for the local alignment of nucleotides and protein sequences.
Source: http://www.ebi.ac.uk/Tools/psa/lalign/
 ProtParam :This software tool gives information about physico-chemical parameters of a protein sequence ,amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.
I had just choose the fasta format of APRT(Human gene) and put my sequence into it.Following are the results obtained from protparam tool.

APRT(human)

RecName: Full=Adenine phosphoribosyltransferase

Fasta format

>gi|114074|sp|P07741.2|APT_HUMAN RecName: Full=Adenine phosphoribosyltransferase; Short=APRT

MADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE

Number of amino acids: 180

Molecular weight: 19607.7

Amino acid composition: 

Ala (A)  16      8.9%

Arg (R)  12      6.7%

Asn (N)   1      0.6%

Asp (D)   9      5.0%

Cys (C)   3      1.7%

Gln (Q)   7      3.9%

Glu (E)  13      7.2%

Gly (G)  17      9.4%

His (H)   2      1.1%

Ile (I)   7      3.9%

Leu (L)  29     16.1%

Lys (K)   8      4.4%

Met (M)   2      1.1%

Phe (F)   8      4.4%

Pro (P)  11      6.1%

Ser (S)  11      6.1%

Thr (T)   6      3.3%

Trp (W)   1      0.6%

Tyr (Y)   4      2.2%

Val (V)  13      7.2%

Pyl (O)   0      0.0%

Sec (U)   0      0.0%

 (B)   0         0.0%

 (Z)   0         0.0%

 (X)   0         0.0%

Total number of negatively charged residues (Asp + Glu): 22

Total number of positively charged residues (Arg + Lys): 20

Atomic composition:

Carbon      C         885

Hydrogen    H        1423

Nitrogen    N         237

Oxygen      O         254

Sulfur      S           5

Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient    11585

Abs 0.1% (=1 g/l)   0.591, assuming all pairs of Cys residues form cystinesExt. coefficient    11460

Abs 0.1% (=1 g/l)   0.584, assuming all Cys residues are reduced

Instability index:

The instability index (II) is computed to be 39.29

This classifies the protein as stable.

Source: http://web.expasy.org/protparam/