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.
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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:
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:
#!/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 (-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:
Last edited Mon Mar 29 2021