Blast

Overview

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

More information is available on the Blast web site: https://blast.ncbi.nlm.nih.gov/Blast.cgi

Usage

First you need to decide on the version of the software you want to use. Use

$ module avail blast

to check what versions are available. We normally recommend using the latest version available. For example, to load the version 2.11,0 use

$ module load blast/2.11.0

For more details on using modules see our modules help guide.

An example PBS script:

#!/bin/bash

#PBS -q normal
#PBS -l ncpus=4
#PBS -l mem=16GB
#PBS -l walltime=02:00:00
#PBS -l wd

# Must include `#PBS -l storage=scratch/ab12+gdata/yz98` if the job
# needs access to `/scratch/ab12/` and `/g/data/yz98/`. Details on:
# https://opus.nci.org.au/display/Help/PBS+Directives+Explained

# Load module, always specify version number.
module load blast/2.11.0

blastx -query /path/to/seq/fasta -db /path/to/DB -evalue 1e-6 -num_threads 4 -max_target_seqs 10000