BLAST

Legacy documentation This page describes a service provided by a retired ACENET system. Most ACENET services are currently provided by national systems, for which please visit https://docs.computecanada.ca.

Description

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Modulefile

blast

Databases

Current, only the NR database is available at ACENET, and its location is stored in the environment variable BLASTDB. See examples below on how to access the database.

Documentation

NCBI BLAST homepage

Usage

Here is an example of a submission script to run BLAST serially:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -j y

module load blast
blastx -query query.FASTA -db $NCBIDB/nr -out ${JOB_ID}_results.txt \
    -evalue 1E-10 -outfmt 7 -num_alignments 10

Here is an example of a submission script how to run BLAST in parallel with 4 threads:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -j y
#$ -pe openmp 4

module load blast
blastx -query query.FASTA -db $NCBIDB/nr -out ${JOB_ID}_results.txt \
    -evalue 1E-10 -outfmt 7 -num_alignments 10 -num_threads $NSLOTS