BLAST

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing biological sequences, such as the amino-acid sequences of different proteins or the DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if human beings carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.

BLAST is one of the most widely used bioinformatics programs, probably because it addresses a fundamental problem and the algorithm emphasizes speed over sensitivity. This emphasis on speed is vital to making the algorithm practical on the huge genome databases currently available, although subsequent algorithms can be even faster.

-- from Wikipedia entry on BLAST

Software

BLAST standalones can be downloaded from http://www.ncbi.nlm.nih.gov/BLAST/download.shtml

A non-command line version, called wwwblast can also be setup so that BLAST of custom databases can be undertaken by using an internet browser.

Scoring Matrices

ftp://ftp.ncbi.nih.gov/blast/matrices/

• BLOSUM62 is the usual scoring matrix used for amino acid sequences

Parsing of Output

BioPython, BioPerl, and BioJava have modules that extraordinarily simplify BLAST parsing in a variety of formats. A HOWTO on BLAST parsing in BioPerl illustrates the power of scripting this parsing.

More information @OpenWetWare

• Wikiomics:BLAST_tutorial
• Wikiomics:BLAST

Parallel BLAST

MPI-BLAST is quite good, but not very robust.

Databases

See ftp://ftp.ncbi.nih.gov/blast/db/

• NR is one of the most important databases.
• Individual Genomes can be downloaded from ftp://ftp.ncbi.nih.gov/genomes/
• Bacterial Genomes : ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

References

• 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.
• Altschul SF, Madden TL, Schaffer 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.
• McGinnis S and Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004 Jul 1; 32(Web Server issue) W20-5. doi:10.1093/nar/gkh435 pmid:15215342.
• Korf I, Yandell M, and Bedell J, BLAST O'Reilly & Associates, 2003.

External Links

• NCBI-BLAST website
• NCBI-BLAST Tutorial
• WU-BLAST (Another implementation of BLAST maintained by Warren Gish at Washington University)
• NBIC mpiBLAST (Netherlands Bioinformatics Centre, running mpiBLAST)
• Parallel BLAST A dual scheduling BLAST tested on the Blue Gene/L
• BLAST HOWTO at the Wikiomics bioinformatics wiki