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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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-apps module.

Usage

Exonerate is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Exonerate module:

module load bio-apps/v202603
module load exonerate/2.4.0

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:

exonerate --model est2genome query.fasta target.fasta

You can see the command line options for exonerate with the command:

exonerate -h

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:

sbatch batch_job_file.sh

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information