From Documentation
Revision as of 11:04, 26 March 2012 by Isaac (Talk | contribs) (Created page with "{{Software |package_name=BLAST |package_description=Suite of programs that allow users to carry out molecular dynamics simulations |package_idnumber=9 }} NCBI BLAST is installed...")

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
Description: Suite of programs that allow users to carry out molecular dynamics simulations
SHARCNET Package information: see BLAST software page in web portal
Full list of SHARCNET supported software

NCBI BLAST is installed under _/opt/sharcnet/blast/current_ on all of SHARCNETs XC clusters as well as various other clusters specified in the Availability Table.

The current directory for BLAST contains four sub-directories named _bin_, _data_, _doc_ and _lib_, where the data directory contains BLOSUM and PAM matrices. This data directory can also be shared with the mpiBLAST package as discussed in the mpiBLAST FAQ. The _bin_ directory contains all the blast binaries, such as @blastall@. This directory is included in your default search path.

Since blast is a serial application jobs should ideally be only run on whale cluster. For example serial jobs can be submitted as follows:

pre{font-size:90%}. sqsub -r 5d -o ofile%J blastall -p blastn -i ech_query.fas -d yeast.nt -o blastn_test.typ sqsub -r 5d -o ofile%J blastall -p blastx -i ech_query.fas -d yeast.aa -o blastx_test.typ sqsub -r 5d -o ofile%J blastall -p tblastn -i test3.aa -d yeast.nt -o tblastn_test.typ sqsub -r 5d -o ofile%J blastall -p blastp -i test3.aa -d yeast.aa -o blastp_test.typ sqsub -r 5d -o ofile%J blastall -p tblastx -i ech_query.fas -d yeast.nt -o tblastx_test.typ

Before running jobs, create a _~/.ncbirc_ file in your home account containing something like:

pre. [NCBI] Data=/opt/sharcnet/blast/current/data [BLAST] BLASTDB=/work/username/your/db/directory BLASTMAT=/opt/sharcnet/blast/current/data

Features available in the currently installed version(s) are shown "here":