BLAST

From BioPerl

BLAST - Basic Local Alignment Search Tool [1, 2] - is one of the most widely used tools in modern bioinformatics. It provides fast identification of similar sequences in a database. The BLAST package for different operating systems can be downloaded at NCBI. See Wikipedia and Wikiomics entries for a good introduction.

In BioPerl, the BLAST application can be run using Bio::Tools::Run::StandAloneBlast, and output parsed using Bio::SearchIO.

BLAST "flavors"

The original NCBI BLAST has inspired various clones, forks and off-shoots implementations - here are some of them:

• NCBI BLAST is distributed by the NCBI.
• WU BLAST is distributed by Warren Gish from Washington University.
• FSA-BLAST is distributed by Michael Cameron from http://www.fsa-blast.org/.
• mpiBLAST by Aaron Darling and collegues from http://mpiblast.lanl.gov/.

BLAST resources

Also see the BLAST book by Ian Korf, Mark Yandell, and Joseph Bedell.

ISBN 0596002998

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References

1. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. Basic local alignment search tool. J Mol Biol 1990 Oct 5; 215(3) 403-10. doi:10.1006/jmbi.1990.9999 pmid:2231712. PubMed HubMed [blast90]
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997 Sep 1; 25(17) 3389-402. pmid:9254694. PubMed HubMed [blast98]

All Medline abstracts: PubMed HubMed