MEME Suite protocols

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MEME Suite statistics

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Popular tool citations

chevron_left Transcription factor binding site prediction De novo motif discovery Differential motif enrichment analysis chevron_right
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Associated diseases

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MEME Suite specifications


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


  • fimo


  • person_outline Timothy L. Bailey <>

Publications for MEME Suite


The MEME Suite.

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

MEME Suite in pipelines

PMCID: 5786225
PMID: 29325123
DOI: 10.1093/gbe/evy005

[…] tool phast () was used to identify phage derived genes in the genome of d. shibae., dna sequence of the seven dsgta coverage peaks was used as primary input for the motif discovery algorithm of the meme suite 4.12.0 (). motif discovery was run in the discriminative mode, with the seven peak regions indicated in as query input and either the whole chromosomal dna sequence or dna sequences […]

PMCID: 5818429
PMID: 29497429
DOI: 10.3389/fpls.2018.00166

[…] | amino acid sequence alignment and pspg box of csugt76f1 and six homologies. the multiple alignment was performed using clustalw2 software. pspg box logo was produced by using meme software ( ()., table s1 | primers sequences used in experiments., table s2 | identification of flavonoids in fruit peels of sweet orange by uplc-q-tof-ms., table s3 | ms analyses of products […]

PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] of the nervous system including neuronal differentiation, migration and fate specification ()., we also used meme (), tomtom () and gomo (), three motif-based sequence analysis tools from the meme suite of programs to analyse the upstream regulatory region in human, mouse and fugu. meme () identifies motifs based on the assumption that tf motifs are more likely to be conserved […]

PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] region in human, mouse and fugu using matinspector () identified several conserved tf binding sites which have relevance for cns-specific expression of c9orf72 (). similar to matinspector, the meme suite of programs, used for regulatory sequence analysis, also identified tf binding motifs that associate with genes involved in regulation of neuronal differentiation and axon guidance ()., […]

PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] and non-aligned upstream region of the three species) by matinspector using matrix family library version 11.0., meme (), tomtom () and gomo (), three motif-based sequence analysis tools from the meme suite of programs, were used to analyze the upstream regulatory region in human, mouse and fugu. meme () was used to identify new ungapped motifs of recurring fixed-length patterns in the chosen […]

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MEME Suite in publications

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] and all 5′ utrs and transcription start sites were manually verified in ugene (). these extracted sequences were then subjected to a motif search using the meme suite (, )., read and contig data sets are available from ncbi under the following bioproject accession numbers: prjna421889 (wastewater data), prjna421892 (sediment data), and prjna421894 […]

PMCID: 5956150
PMID: 29769381
DOI: 10.1128/mSphere.00222-18

[…] expressed genes (11.5%; n = 52) (see and  in the supplemental material)., putative tosr binding consensus sequence. multiple em for motif elicitation software (meme version 4.12.0, was used to identify a 29-bp consensus sequence enriched in the upstream regions of a subset of differentially regulated genes (44.9%; n = 129) relative to nondifferentially regulated […]

PMCID: 5940787
PMID: 29739980
DOI: 10.1038/s41598-018-25315-w

[…] function of these domains in 5 mc excision.figure 2, in order to further determine the conservation and divergence of plant dmls, we searched conserved motifs in smdmls, atdmls and osdmls using the meme suite ( a total of 15 conserved motifs were identified (fig. ). the length of motifs ranges from 18 to 150 amino acids (table ). the number of motifs […]

PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0

[…] test (alrt) and depends on a non-parametric shimodaira-hasegawa-like (sh-like) approach., a search for conserved motifs within hvspl proteins was performed by using the meme 4.11.0 tool (, using default settings, except that the maximum width was 50, the minimum width was 6, and the maximum number of motifs to find was 10. the online weblogo3 platform […]

PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] gene were extracted from the genome and used as the promoter sequences. tss of each annotated gene has been predicted by gene prediction software in previous study []. for motif analysis, tools of meme suite (v.4.12.0) were used with default settings []. motif discovery was performed with discriminative regular expression motif elicitation (dreme) with entire homoeologous gene promoters […]

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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.