BLAST

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.

Availability & Restrictions

BLAST is available without restriction to all OSC users.

The following versions of BLAST are available on OSC systems:

Version Oakley Owens
2.2.24+ X  
2.2.25+ X  
2.2.26 X  
2.2.31+ X  
2.4.0+   X*
2.6.0+ X*  

 

If you need to use blastx, you will need to load one of the C++ implimenations modules of blast (any version with a "+").

Set-up

To load BLAST, type the following into the command line:

module load blast

Then create a resource file .ncbirc, and put it under your home directory.

Using BLAST

The five flavors of BLAST mentioned above 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 nt and refseq_protein databases. You can access the database using BLASTDB environment variable. If you need other databases, please send a request email to OSC Help .

Batch Usage

A sample batch script is below:

#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00
#PBS -N Blast
#PBS -S /bin/bash
#PBS -j oe
module load blast
set -x
cd $PBS_O_WORKDIR
mkdir $PBS_JOBID
cp 100.fasta $TMPDIR
cd $TMPDIR
/usr/bin/time blastn -db nt -query 100.fasta -out test.out
cp test.out $PBS_O_WORKDIR/$PBS_JOBID

NCBI BLAST Database

The NCBI BLAST database is updated on Oct 30th 2017 and is available  at /fs/project/pub_data/blastDB-Oct2017/db  

Further Reading

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