BLAST

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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, a local BLAST application can be run using Bio::Tools::Run::StandAloneBlast, and output parsed using Bio::SearchIO.

To run BLAST on the remote NCBI servers, use Bio::Tools::Run::RemoteBlast.

Contents

BLAST "flavors"

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

AB-BLAST represents the future direction of WU-BLAST. For more information about the software, please see http://blast.advbiocomp.com/doc/README.html (email of 14 Oct 2009)

BLAST resources

Tutorials

Book

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

OReillyBLASTBookCover.jpg ISBN 0596002998

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:10.1016/S0022-2836(05)80360-2 | PubMed ID:2231712 | 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. PubMed ID:9254694 | HubMed [blast98]
All Medline abstracts: PubMed | HubMed
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