Software Tools

Matlab Bioinformatics Toolbox
www.mathworks.com/products/bioinfo/

Software Tools for Sequence Analysis:

  • AceDB – a tool for viewing and managing genomic data
    www.acedb.org
  • Artemis / ACT – Artemis: genome viewer and annotation tool, and ACT: (Artemis Comparison Tool) a DNA sequence comparison viewer based on Artemis
    www.sanger.ac.uk/Software/Artemis
  • BLAST – Basic Local Alignment Search Tool for sequence similarity searching against nucleotide and protein databases
    www.ncbi.nlm.nih.gov/BLAST
  • bl2seq – compare two sequences using BLAST (both sequences either protein or nucleotide)
  • ClustalW – multiple sequence alignment program for DNA/proteins. Graphic interface, ClustalX, also available
  • EMBOSS – a suite of around 100 bioinformatics tools
  • FASTA – Sequence similarity searching against nucleotide and protein databases
  • formatdb – Prepare a nucleotide or protein sequence file for seaching using BLAST
    www.ncbi.nlm.nih.gov/BLAST/docs/formatdb.html
  • Glimmer – (Gene Locator and Interpolated Markov Modeler) a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
    www.tigr.org/software/glimmer
  • GENSCAN – predicts the locations and exon-intron structures of genes in genomic DNA
    genes.mit.edu/GENSCAN.html
  • Jalview – a multiple sequence alignment editor written in java
    www.jalview.org
  • MSPcrunch – a BLAST output filtering tool
    www.cgb.ki.se/cgb/groups/sonnhammer/MSPcrunch.html
  • MUMmer – a system for rapidly aligning entire genomes
    www.tigr.org/software/mummer
  • OligoArray – computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
    berry.engin.umich.edu/oligoarray2
  • Phred, Phrap and Consed – Phred: reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base; Phrap: assembles shotgun DNA sequence data using the base calls and base quality values produced by Phred; Consed: a tool for viewing, editing, and finishing sequence assemblies created with Phrap
    www.phrap.org
  • Primer3 – design primers within a DNA sequence
    frodo.wi.mit.edu/primer3/primer3_code.html
  • RepeatMasker – screens DNA sequences for interspersed repeats and low complexity DNA sequences
    www.repeatmasker.org
  • Readseq – reads sequence files and interconverts between many different sequence file formats
    iubio.bio.indiana.edu/soft/molbio/readseq/version2/Readseq2-help.html
  • sim4 – aligns an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
    globin.cse.psu.edu/html/docs/sim4.html
  • SRS – (Sequence Retieval System) for database and cross-database querying
    https://zen.molbiol.ox.ac.uk/srs-7.1.3.1/cgi-bin/wgetz?-page+srsq2+-noSession
  • Staden – a set of DNA sequence assembly, editing and analysis tools
    staden.sourceforge.net
  • STARS – an alternative interface to Staden for sequence assembly of sequence typing projects
    – External link: www.molbiol.ox.ac.uk/~paediat/stars/index.html
  • T-COFFEE – a DNA or protein multiple sequence alignment package
    – External link: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
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