Difference between revisions of "Applications/Cegma"
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==Application Details== | ==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 | + | *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. |
| − | any eukaryotic genome. | ||
*Version: 2.5.0 | *Version: 2.5.0 | ||
*Module: cegma/2.5.0 | *Module: cegma/2.5.0 | ||
| − | *Licence: | + | *Licence: Open source, free to academic research |
==Usage Examples== | ==Usage Examples== | ||
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===Module=== | ===Module=== | ||
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<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
[username@login01 ~]$ module add cegma/2.5.0 | [username@login01 ~]$ module add cegma/2.5.0 | ||
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</pre> | </pre> | ||
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| − | + | ==Further Information== | |
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| + | * [http://korflab.ucdavis.edu/datasets/cegma/ http://korflab.ucdavis.edu/datasets/cegma/] | ||
| + | ==Navigation== | ||
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* [[Main_Page|Home]] | * [[Main_Page|Home]] | ||
| − | * [[Applications|Application support]] | + | * [[Applications|Application support]] * |
* [[General|General]] | * [[General|General]] | ||
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* [[Programming|Programming support]] | * [[Programming|Programming support]] | ||
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Latest revision as of 11:16, 24 May 2019
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