Bioinformatics Softwares

BIOINFORMATICS SOFTWARES DOWNLOADS

The use of software in biological applications has given a new dimension to the field of bioinformatics. Freeware software is available on the internet and many universities have established servers. There are number of simple stand-alone programs as well as complex integrated network version of the commercial software available. But keeping track of all the programmes is difficult task; here I have reproduced the comprehensive list of some of the common bioinformatics software's. Although it should not be taken as exhaustive list, I hope it be useful to scientist/students from life science as well as bioinformatics (beginner to intermediate level) stream.

Here is the list of some common bioinformatics software's used. This list includes Windows version, Linux and Mac version only. The criteria for selecting bioinformatics software's

1. Software should be accessible to all, easy to use and should run on normal PC . Maximum concentrated on GUI interface and to some extent DOS commands to avoid command interface.

2. Software list selected below to run some of common tasks in bioinformatics, which should be usable to person from varied fields from life sciences/molecular biology background.

3. Last but not the least, software's should be easy to install with out complex commands.

Prerequisite:

• Familiarity to use Operating system and to know unzip or to run exe files
  
  Alignment/Similarity Search Tools

EBI- Fasta executable: Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. Fasta can be very specific when identifying long regions of low similarity especially for highly diverged sequences.Download EBI-Fasta executable via FTP

EBI-Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.Download EBI-Clustal W via FTP

Clustal X: Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. Download Clustax (Windows OS)

TIGR-MUMmer(fast alignment of large-scale DNA and protein sequences):A system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides. Download MUMer Via FTP

TIGR-AAT package(A tool for analyzing and annotating genomic sequences): The AAT package includes two sets of programs, one set (DPS/NAP) for comparing the query sequence with a protein database, and the other (DDS/GAP2) for comparing the query with a cDNA databa(Huang et al., 1997).Download AAT package via FTP


Gene Structure Prediction Tools

TIGR-Glimmer: Glimmer are for identification of possible genes for prokaryotes sequences . It is based on interpolated Markov models to identify the coding regions and distinguish them from noncoding DNA.Download Glimmer Via FTP

TIGR-GlimmerM: A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. Download Glimmer Via FTP