MEME Suite statistics

Tool stats & trends

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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 FIMO Team
  • 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 citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] ://, 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 (, ). […]


Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] 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 (http:/ […]


Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

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

[…] ch 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 and ext […]


Molecular Characterization of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) Gene Family in Betula luminifera

Front Plant Sci
PMCID: 5945835
PMID: 29780401
DOI: 10.3389/fpls.2018.00608

[…] SBP domains, ANK domains and miR156 complementary sequences was carried out using Vector NTI 11.0 (Invitrogen). Conserved motifs were determined using MEME version 4.11.4 (Bailey and Elkan, ) ( with the parameters as previous study (Li and Lu, ). MiR156-targeted BlSPLs were predicted using psRNATarget tool (; Dai and Zhao, ). […]


Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] ligned to construct phylogenetic tree using MEGA v6.0 with automatic bootstrap criteria (Maximum Likelihood) (Tamura et al., ). The conserved motifs of top 20 homologies NBS-LRR were identified using MEME suite (Bailey et al., ; Supplementary File : Figure S26).Nodulation regulatory and nodulin genes were identified based on GO analyses. The GO IDs for each gene were obtained through BLAST search […]


Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] ential function of proteins. The functionally conserved motifs in both SolyWRKY33 and SolyWRKY37 proteins were investigated using MEME (Multiple Expectation Maximization for Motif Elicitation ( tool []. The number of potential motifs was set up to 10 with having an optimum motif width ranging between 10 and 30 residues, with zero or one occurrence per sequence. The […]


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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.