MEME Suite protocols

MEME Suite specifications

Information


Unique identifier OMICS_00497
Name MEME Suite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 4.10.1
Stability Stable
Maintained Yes

Subtool


  • fimo

Maintainer


  • person_outline Timothy L. Bailey <>

Publications for MEME Suite

library_books

The MEME Suite.

2015 Nucleic Acids Res
PMCID: 4489269
PMID: 25953851
DOI: 10.1093/nar/gkv416

MEME Suite IN pipelines

 (7)
2017
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] of kernel density was then plotted as a metagene. analysis of motif enrichment was performed on the sense dna sequence ±2 nucleotides up- and down-stream of the called truncation sites using the meme suite., relative levels of internal m6a was determined by thin layer chromatography (tlc) as described previously35. m6a measured using tlc does not have the problem of potential contamination […]

2017
PMCID: 5703070
PMID: 28459457
DOI: 10.1038/ng.3844

[…] to link dux4 peak regions to annotated genes (basal plus extension; proximal 5kb upstream, 1kb downstream, plus distal up to 15kb). motif discovery and enrichment analyses were performed with the meme suite tools (mchanick and bailey, 2011). to evaluate enrichment at repeat elements, alignment files were filtered using samtools (view –q 10) to remove lower quality, multi-mapping reads. […]

2017
PMCID: 5703070
PMID: 28459457
DOI: 10.1038/ng.3844

[…] to link (ha) dux peak regions to annotated genes (basal plus extension; proximal 5kb upstream, 1kb downstream, plus distal up to 15kb). motif discovery and enrichment analyses performed using the meme suite tools. to evaluate enrichment at repeat elements, alignment files were filtered using samtools (view –q 10) to remove lower quality, multi-mapping reads. over-representation of particular […]

2016
PMCID: 4977670
PMID: 27503086
DOI: 10.1186/s12864-016-2916-7

[…] were retrieved using the ensembl plants database [38], via its perl api (application program interface)., to predict tfbss in the upstream promoter regions, we installed a standalone version of the meme suite, which includes the fimo motif search tool [28, 39]. for this fimo motif discovery, we first collected a non-redundant set of position-weight matrices (pwms) for binding profiles of known […]

2016
PMCID: 5103509
PMID: 27829357
DOI: 10.1186/s12864-016-3248-3

[…] one treatment group as control and comparing the other treatment group to the corresponding control. coverage was determined by normalizing the total number of mapped reads per hundred million. meme suite (version 4.10.1) was used for motif discovery. the ±100 bp around a peak summit was used for motif discovery. annotated genes with its 50 kb upstream that overlapped with erα peaks […]

MEME Suite institution(s)
Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia

MEME Suite review

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Ka-Chun Wong's avatar image No country

Ka-Chun Wong

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The MEME suite for motif discovery and search is the most popular software for motif discovery. Its pattern recognition ability is one of the best tools I have ever seen. I highly recommend the suite. To be fair, I would also like to note the slightly high computational complexity exist in some of the programs (e.g. long running time). The users need to be aware of it.