MEME protocols

MEME specifications

Information


Unique identifier OMICS_08103
Name MEME
Alternative names Multiple Em for Motif Elicitation, CUDA–MEME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Multiple_EM_for_Motif_Elicitation

Download


Versioning


Add your version

Maintainer


  • person_outline FIMO Team <>

Additional information


A CUDA implementation is also available here : https://doi.org/10.1016/j.patrec.2009.10.009

Information


Unique identifier OMICS_08103
Name MEME
Alternative names Multiple Em for Motif Elicitation, CUDA–MEME
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Multiple_EM_for_Motif_Elicitation

Maintainer


  • person_outline FIMO Team <>

Additional information


A CUDA implementation is also available here : https://doi.org/10.1016/j.patrec.2009.10.009

Publication for Multiple Em for Motif Elicitation

MEME IN pipelines

 (40)
2017
PMCID: 5294834
PMID: 28166727
DOI: 10.1186/s12864-017-3523-y

[…] using clustal-omega and reconstructed a phylogenetic tree using mega6 [47]. for each subfamily, we identified the most conservative motifs on the published vir genes in each subfamilies using meme [48], and confirmed that these motifs exist in our novel genes (fig. 6). our analyses revealed that the proportion of novel vir genes assigned to subfamilies were quite different and suggested […]

2017
PMCID: 5744064
PMID: 29312251
DOI: 10.3389/fmicb.2017.02573

[…] acid sequence alignments of czoa with representative class a β-lactamases and czor with its homologs were conducted using clustal omega1. the iscr-binding site was analyzed by the online program meme2 (bailey and elkan, 1994). the -35 and -10 sequences were predicted using softberry bprom tool3 (solovyev and salamov, 2011)., the iscr-mutant strain iscr-280 and its complemented strain […]

2016
PMCID: 4794789
PMID: 27047744
DOI: 10.1002/2211-5463.12022

[…] within the alignment were analysed for structural or functional significance. molecular visualization was performed using rasmol 54. analysis of conserved sequence motifs was facilitated by meme program 55. group entropy analysis (gent) 47 was performed to compare udpgdh, udpnamdh and gdpmdh groups to each other., the phylip suite of programs was used to generate the phylogenetic tree […]

2016
PMCID: 4889651
PMID: 27172209
DOI: 10.1534/g3.116.029181

[…] [500 bp upstream of start codons for gene models, upstream regions to transcription start sites (tsss), 5′-/3′-utrs, whole gene models and coding sequences (cdss)] were retrieved using biomart. meme (multiple expectation maximization for motif elicitation; bailey and elkan 1994) was used to find enriched motifs in the 500 bp regions upstream of cdss for the 300 most highly upregulated […]

2015
PMCID: 4314295
PMID: 25622028
DOI: 10.1371/journal.pgen.1004970

[…] the maximum likelihood method. the analysis involved 71 protein sequences. all positions containing gaps and missing data were eliminated. there were a total of 85 positions in the final dataset., meme [51] with default parameters was used to identify statistically significant blocks of sequence homology in n-terminal tails extracted from 67 plant cenh3 sequences available from public […]

MEME institution(s)
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA

MEME review

star_border star_border star_border star_border star_border
star star star star star

Arup Ghosh

star_border star_border star_border star_border star_border
star star star star star
Desktop
Meme is a great suite for motif discovery and annotation from ChIP-seq data. The meme-chip from meme suite can be used for known as well as de novo motif search.