Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

References:

• Slater GS and Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31; doi: 10.1186/1471-2105-6-31

• Exonerate Main Site

• Module Name: exonerate (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load exonerate
[+] Loading exonerate, version 2.2.0...
[user@cn3144 ~]$ exonerate query.fasta target.fasta
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. exonerate.sh). For example:

#!/bin/bash
set -e
module load exonerate
exonerate query.fasta target.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] exonerate.sh

Create a swarmfile (e.g. exonerate.swarm). For example:

exonerate query01.fasta target.fasta
exonerate query02.fasta target.fasta
exonerate query03.fasta target.fasta
exonerate query04.fasta target.fasta

Submit this job using the swarm command.

swarm -f exonerate.swarm [-g #] [-t #] --module exonerate