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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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