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


Version on CSC's Servers

Taito: 2.2.0
FGI grid: 2.2.0


In Taito 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 Taito, 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 Taito, Exronerate should be executed in Taito-shell environment or as a batch . Below is a sample batch job file, for running a Exonerate batch job in Taito:

#!/bin/bash -l
#SBATCH -J exonerate_job
#SBATCH -o output_%j.txt
#SBATCH -e errors_%j.txt
#SBATCH -t 08:00:00
#SBATCH --mem=4000
#SBATCH -p serial
#SBATCH -n 1

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

In the batch job example above, one task (-n 1) is executed. The maximum duration of the job is eight hours (-t 08:00:00 ) and the reserved memory size is about 4 GB (--mem=4000).

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

sbatch batch_job_file.bash

Check the chapter 3 of the Taito user guide for more information about running batch jobs.

Running Exonerate alignments utilizing grid computing

Aligning large amounts of query sequences to a target sequence set can take several hours or even days. Using grid computing through grid_exonerate command you can speed up the alignment process ten fold or more. grid_exonerate command splits the alignment task into several subtasks that it submits to be simultaneously executed in the FGCI grid environment. When all the subtasks are ready they are collected and combined into a single result alignment.

To be able to use grid_exonerate command you should have:

  1. A valid grid certificate installed in the server.
  2. Membership of FGI Virtual Organization

Please check FGCI user guide the detailed instructions to obtain and install a grid certificate and to join FGI Virtual organization.

Once you have the certificate installed and the Virtual organization membership is approved,  you can submit grid_exonerate jobs with for example following commands:

module load biokit

arcproxy -S -c validityPeriod=72h

grid_exonerate --model est2genome --query query.fasta --target target.fasta --out result.out


Note that in the case of grid_exonerate you must always use options --query, --target and --out to define the input and output files.

For more information about grid_exonerate, run command:

grid_exonerate --help

Using Exonerate in FGI

Please check the Exonerate Run Time Environment page for the instructions for using Exonerate in the FGI grid.