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BLAST

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. 

BLAST (including an updated version called BLAST+) is a suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.

Web BLAST is a service at the National Center for Biotechnology Information through which the BLAST programs can be run. A set of databases for use with BLAST is also on the NCBI web site. When referring to BLAST in these notes, we mean a standalone version of the software that has been installed on WestGrid machines, not the Web BLAST service.

As announced in the January 2009 issue of NCBI News, older BLAST software has been rewritten and released as BLAST+. If you have previous experience with BLAST, but, not with BLAST+, please have a look at that announcement. It describes some of the changes in command names that have been introduced with BLAST+.

BLAST exists in both serial and parallel (versions). Users may prefer to run a number of serial jobs simultaneously, rather than use the parallel version of BLAST.

For the versions of BLAST or BLAST+ installed on WestGrid, see the main WestGrid software page.

A user manual and tutorials for the BLAST+ command-line based programs are available from NCBI.

Running BLAST on Breezy

See /global/software/blast and /global/software/ncbi-blast. See /global/software/blast/db for databases.You might also be interested in /global/software/rig and /global/software/GSFLX.

Running BLAST on Bugaboo

BLAST+ (rather than the older BLAST software) has been installed on Bugaboo. The commands (blastn, makeblastdb, legacy_blast.pl, etc.) are on the default command path.

The BLAST databases are in /usr/local/blastdb. In addition open-source parallel BLAST has been installed on Bugaboo. This includes commands mpiblast, mpiformatdb and mpiblast_cleanup on the default command path.

2015-06-15: Added reference to databases on Breezy.