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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


Free to use and open source under GNU GPLv3.


Version on CSC's Servers

Puhti: 2.4.0


In Puhti you can use initialize Exonerate with command:

module load biokit
The biokit module sets up a set of commonly used bioinformatics tools, including Exonerate (Note however that there are also bioinformatics tools in Puhti, that have a separate setup commands.)

After the setup command the Exonerate commands are recognized.

For example to align cDNA to genomic sequence, you can use exonerate command with est2genome model.

exonerate --model est2genome query.fasta target.fasta
You can see the command line options for exonerate with command:
exonerate -h

In Puhti, large Exronerate tasks should be executed as a batch jobs. Below is a sample batch job file, for running a Exonerate batch job in Puhti:

#SBATCH --job-name=exonerate_job
#SBATCH --account=<project>
#SBATCH --time=08:00:00
#SBATCH --mem=8G
#SBATCH --partition=small

module load biokit
exonerate --model est2genome query.fasta target.fasta

In the batch job example above, the maximum duration of the job is eight hours (-t 08:00:00 ) and the reserved memory size is 8 GB (--mem=8G).

You can submit the batch job file to the batch job system with command:

sbatch batch_job_file.bash


Last update: October 10, 2022