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-->
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|{{#vardefine:app|meme}}
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|{{#vardefine:url|http://meme.sdsc.edu/meme/intro.html}}
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<!--CONFIGURATION: OPTIONAL (1=ON)-->
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|{{#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-->
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<!--Description-->
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{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
''The MEME/MAST system allows you to:''
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The MEME Suite allows you to:
 
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* discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences,
# Discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and,
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* search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN,
# Search sequence databases using motifs using MAST.
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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
==Location==
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* analyse motif enrichment using SpaMo or CentriMo.
 
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<!--Modules-->
/apps/meme/4.3.0
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==Required Modules==
 
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[[Modules|modules documentation]]
==Environment==
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===Serial===
 
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*{{#var:app}}
MPI:  
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===Parallel (OpenMPI)===
module load intel/10.1 mvapich/0.9.9
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*gcc/5.2.0
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*openmpi/1.10.2
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*{{#var:app}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_MEME_BIN - executable directory
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<!--Run-->
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{{#if: {{#var: exe}}|==How To Run==
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DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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|}}
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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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-->
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{{#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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|}}
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<!--Installation-->
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{{#if: {{#var: installation}}|==Installation==
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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__NOTOC____NOEDITSECTION__

Latest revision as of 21:21, 6 December 2019

Description

meme 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.

Required Modules

modules documentation

Serial

  • meme

Parallel (OpenMPI)

  • gcc/5.2.0
  • openmpi/1.10.2
  • meme

System Variables

  • HPC_MEME_DIR - installation directory
  • HPC_MEME_BIN - executable directory