Difference between revisions of "Meme"

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==Overview==
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
From the [http://meme.sdsc.edu/meme/intro.html Meme Website]:
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{|<!--CONFIGURATION: REQUIRED-->
 +
|{{#vardefine:app|meme}}
 +
|{{#vardefine:url|http://meme.sdsc.edu/meme/intro.html}}
 +
<!--CONFIGURATION: OPTIONAL (1=ON)-->
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|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
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|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
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|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 +
|{{#vardefine:exe|}} <!--RUNNING -->
 +
|{{#vardefine:conf|}} <!--CONFIGS-->
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|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}} <!--POLICY-->
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|{{#vardefine:testing|}} <!--TESTING/PROFILING-->
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|{{#vardefine:faq|}} <!--FAQ-->
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|{{#vardefine:citation|}} <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
 +
<!--Description-->
 +
{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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The MEME Suite allows you to:
 +
* discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences,
 +
* search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN,
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* compare a motif to all motifs in a database of motifs,
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* associate motifs with Gene Ontology terms via their putative target genes, and
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* analyse motif enrichment using SpaMo or CentriMo.
 +
<!--Location-->
 +
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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<!--Versions-->
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==Available versions==
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* 3.0.13, 4.3.0, 4.6.1 (EL5)
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* 4.8.1 (EL6)
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<!--Modules-->
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{{#if: {{#var: mod}}|==Running the application using modules==
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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* HPC_MEME_BIN - executable directory
  
''The MEME/MAST system allows you to:''
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The core meme module provides single-threaded versions of MEME tools. To make the MPI-enabled ''meme_p'' binary available load the appropriate modules:
 
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module load intel/2012 openmpi/1.6 meme
# Discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and,
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<!--Run-->
# Search sequence databases using motifs using MAST.
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{{#if: {{#var: exe}}|==How To Run==
 
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DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
==Location==
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|}}
 
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<!--Configuration-->
/apps/meme/4.3.0
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{{#if: {{#var: conf}}|==Configuration==
 
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
==Environment==
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|}}
 
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<!--PBS scripts-->
MPI:  
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{{#if: {{#var: pbs}}|==PBS Script Examples==
module load intel/10.1 mvapich/0.9.9
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage policy==
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
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|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
 +
{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
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DOUBLE_CLICK_TO_WRITE_CITATION_HERE
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|}}
 +
<!--Installation-->
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{{#if: {{#var: installation}}|==Installation==
 +
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 +
__NOTOC____NOEDITSECTION__

Revision as of 17:36, 3 August 2012

Description

{{{name}}} website  
The MEME Suite allows you to:

  • discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences,
  • search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN,
  • compare a motif to all motifs in a database of motifs,
  • associate motifs with Gene Ontology terms via their putative target genes, and
  • analyse motif enrichment using SpaMo or CentriMo.

Template:App Location

Available versions

  • 3.0.13, 4.3.0, 4.6.1 (EL5)
  • 4.8.1 (EL6)

Running the application using modules

To use meme with the environment modules system at HPC the following commands are available:

Get module information for meme:

$module spider meme

Load the default application module:

$module load meme

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_MEME_DIR - directory where meme is located.
  • HPC_MEME_BIN - executable directory

The core meme module provides single-threaded versions of MEME tools. To make the MPI-enabled meme_p binary available load the appropriate modules:

module load intel/2012 openmpi/1.6 meme