BLAST

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.

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.
• The Application Formerly Known as WU BLAST was distributed by Warren Gish from Washington University. He has written:

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)

• mpiBLAST by Aaron Darling and collegues from http://mpiblast.lanl.gov/.

BLAST resources

Tutorials

• eTutorial: Basic local alignment search tool (BLAST)

Book

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

ISBN 0596002998

• Find this book on Amazon.com
• Find this book on Barnes & Noble
• Find this book on BooksPrice

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 |
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.