MEME Suite statistics

Tool stats & trends

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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

Maintainers


  • person_outline FIMO Team
  • 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 citations

 (800)
call_split

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

2018
mSystems
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] ://github.com/ajvilleg/extractUpStreamDNA), 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 (, ). […]

call_split

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

2018
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 (http://meme-suite.org/tools/meme), 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:/ […]

library_books

Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

2018
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 […]

library_books

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

2018
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, ) (http://meme-suite.org/tools/meme) with the parameters as previous study (Li and Lu, ). MiR156-targeted BlSPLs were predicted using psRNATarget tool (http://plantgrn.noble.org/psRNATarget/; Dai and Zhao, ). […]

library_books

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

2018
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 […]

library_books

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

2018
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 (http://meme-suite.org/tools/meme) 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 […]

Citations

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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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Web
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.