BLAST
Introduction
The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be
thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.
The five flavours of BLAST perform the following tasks:
- blastp
compares an amino acid query sequence against a protein sequence database
- blastn
compares a nucleotide query sequence against a nucleotide sequence database
- blastx
compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database
- tblastn
compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
- tblastx
compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. (Due to the nature of tblastx, gapped alignments are not available with this option)
We provide local access to nr and swissprot databases. Other databases are available upon request.
Version
Version 2.2.17 is currently available at OSC.
Availability
The BLAST package is available on the Glenn Cluster.
Usage
To use the BLAST commands, first load the blast module into your shell environment:
module load biosoftw
module load blast
Then create a resource file , and put it under your home directory.
The contents of the file are just these two lines:
[NCBI]
Data="/usr/local/biosoftw/blast-2.2.17/data/"
[BLAST]
BLASTDB="/usr/local/biosoftw/db/"
Documentation
More information can be found at the NCBI Blast server http://blast.ncbi.nlm.nih.gov/Blast.cgi.
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