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Exonerate at CSC

A generic tool for pairwise sequce comarison

Versions

Exonerate version 2.2.0  is available in Hippu and Vuori.

Exonerate version 1.4.0  is available in Murska.


Description

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

Using Exonerate


For command line usage, the setup command for Exonerate in Hippu, Vuori or  Murska is:

module load exonerate

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


More information


Mattila Kimmo Kimmo.Mattila at csc.fi
Saren Ari-Matti Ari-Matti.Saren at csc.fi