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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

Puhti: 2.4.0

Usage

On Puhti, you can initialize Exonerate with the command:

module load biokit

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

After loading the biokit module, 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 the command:

exonerate -h

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

#!/bin/bash
#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 (--time=08:00:00) and the reserved memory is 8 GB (--mem=8G).

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

sbatch batch_job_file.bash

More information