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