Exonerate
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. You can use Exonerate for example for:
- Aligning a cDNA to a genomic sequence
- Aligning a protein to genomic sequence
- 6-frame translated alignment
- Genome to genome alignment
- Exhaustive Smith-Waterman-Gotoh alignment
License
Free to use and open source under GNU GPLv3.
Available
- Roihu: 2.4.0, via the
bio-appsmodule.
Usage
Exonerate is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Exonerate module:
After loading, the exonerate commands are recognized.
For example, to align cDNA to genomic sequence, you can use the exonerate command with the est2genome model:
You can see the command line options for exonerate with the command:
Large Exonerate tasks should be executed as batch jobs. Below is a sample batch job script for running an Exonerate batch job on Roihu:
#!/bin/bash
#SBATCH --job-name=exonerate_job
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --time=08:00:00
#SBATCH --partition=small
#SBATCH --mem=8G
module load bio-apps/v202603
module load exonerate/2.4.0
exonerate --model est2genome query.fasta target.fasta
In the batch job example above, the maximum duration of the job is eight hours (--time=08:00:00) and the reserved memory is 8 GB (--mem=8G). Replace <project> with your CSC project (for example project_2001234).
You can submit the batch job file to the batch job system with the command:
See creating a batch job script for Roihu for more information about running batch jobs.