he 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
The following versions of BLAST are available on OSC systems:
You can use
module spider blast to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
If you need to use blastx, you will need to load one of the C++ implimenations modules of blast (any version with a "+").
BLAST is available without restriction to all OSC users.
Publisher/Vendor/Repository and License Type
National Institutes of Health, Open source
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.
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)
NCBI BLAST Database
Information on the NCBI BLAST database can be found here. https://www.osc.edu/resources/available_software/scientific_database_list/blast_database
We provide local access to nt and refseq_protein databases. You can access the database by loading desired blast-database modules. If you need other databases, please send a request email to OSC Help .
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 module load blast-database 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