Applications/Cegma - Revision history

Pysdlb at 11:16, 24 May 2019

2019-05-24T11:16:17Z

Pysdlb at 11:08, 24 April 2017

2017-04-24T11:08:08Z

Pysdlb: Pysdlb moved page Cegma to Applications/Cegma without leaving a redirect

2017-04-24T11:06:07Z

Pysdlb moved page Cegma to Applications/Cegma without leaving a redirect

Pysdlb at 11:05, 24 April 2017

2017-04-24T11:05:36Z

Pysdlb at 11:05, 24 April 2017

2017-04-24T11:05:18Z

Pysdlb at 11:03, 24 April 2017

2017-04-24T11:03:54Z

Pysdlb: Created page with "TOC ==Application Details== *Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virt..."

2017-04-24T11:03:19Z

Created page with "__TOC__ ==Application Details== *Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virt..."

New page

__TOC__

==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: GNU

==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===
<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 ~]$ cegma --genome sample.dna --protein sample.prot -o sample
</pre>

===Compilation===

''boost'' is a library for use either with a compiled binary that requires it, or it could be required at compilation time also.

A typical code snippet requiring is shown below:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

</pre>

==Further Information==

* [https://support.hdfgroup.org/HDF5/ https://support.hdfgroup.org/HDF5/]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 38: / Line 38: @@
 * [http://korflab.ucdavis.edu/datasets/cegma/ http://korflab.ucdavis.edu/datasets/cegma/]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 36: / Line 36: @@
 ==Further Information==
-* [https://support.hdfgroup.org/HDF5/ https://support.hdfgroup.org/HDF5/]
+* [http://korflab.ucdavis.edu/datasets/cegma/ http://korflab.ucdavis.edu/datasets/cegma/]
 {|

← Older revision	Revision as of 11:06, 24 April 2017
(No difference)

@@ Line 2: / Line 2: @@
 ==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.
 *Version: 2.5.0
 *Module: cegma/2.5.0

@@ Line 6: / Line 6: @@
 *Version: 2.5.0
 *Module: cegma/2.5.0
-*Licence: GNU
+*Licence: Open source, free to academic research
 ==Usage Examples==

@@ Line 25: / Line 25: @@
 ===Module===
 <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@login01 ~]$ module add cegma/2.5.0
@@ Line 30: / Line 32: @@
 </pre>

Applications/Cegma - Revision history

Pysdlb at 11:16, 24 May 2019

Pysdlb at 11:08, 24 April 2017

Pysdlb: Pysdlb moved page Cegma to Applications/Cegma without leaving a redirect

Pysdlb at 11:05, 24 April 2017

Pysdlb at 11:05, 24 April 2017

Pysdlb at 11:03, 24 April 2017

Pysdlb: Created page with "__TOC__ ==Application Details== *Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virt..."

Pysdlb: Created page with "TOC ==Application Details== *Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virt..."