Applications/Cegma

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Application Details

  • Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.
  • Version: 2.5.0
  • Module: cegma/2.5.0
  • Licence: Open source, free to academic research

Usage Examples

CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. We use the KOGs database to build a set of these highly conserved ubiquitous proteins. We define a set of 458 core proteins, and the protocol, CEGMA, to find orthologs of the core proteins in new genomes and to determine their exon-intron structures.

It has the following commands:

  • cegma
  • completeness
  • geneid-train
  • genome_map
  • hmm_select
  • local_map
  • make_paramfile parsewise

and is invoke by loading the cegma module within Viper.

Module

[username@login01 ~]$ module add cegma/2.5.0
[username@login01 ~]$ cegma --genome sample.dna --protein sample.prot -o sample



Further Information

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