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
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.
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)
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 .
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
Information on the NCBI BLAST database can be found here. https://www.osc.edu/resources/available_software/scientific_database_list/blast_database