MEME statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MEME
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Tool usage distribution map

This map represents all the scientific publications referring to MEME per scientific context
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Associated diseases

This word cloud represents MEME usage per disease context
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Popular tool citations

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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

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Versioning


No version available

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

Publications for Multiple Em for Motif Elicitation

MEME citations

 (719)
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 […]

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

[…] ://weblogo.berkeley.edu/). Sequence alignment of 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://pl […]

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

[…] cbi.pku.edu.cn/). The predicted genes were used to BLAST search against the PlantTFDB (E-value: 1e-10). The FAR1 motif was predicted using the Multiple Expectation Maximization for Motif Elicitation (MEME)/Motif Alignment and Search Tool (MAST) system (http://meme-suite.org/) (Bailey et al., ) and visualized using the TBtools (version 0.4999) (https://github.com/CJ-Chen/TBtools). […]

library_books

Genome wide analysis of the NAC transcription factor family and their expression during the development and ripening of the Fragaria × ananassa fruits

2018
PLoS One
PMCID: 5933797
PMID: 29723301
DOI: 10.1371/journal.pone.0196953

[…] gions containing only the NAC multi-domains, and iii) the carboxyl terminal (TR) regions lacking the NAC multi-domains. The amino terminal region harboring the NAC domain was identified after running MEME to recognize the limits of the conserved domains and considering the information provided into the CDD database. Eventually, we run a Clustal Omega alignment with the entire NAC sequences from an […]

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

[…] The MEME motif scan analysis revealed the presence of uniform motifs across all the members in SolyWRKY33. The phylogenetic studies revealed the monophyletic origin of SolyWRKY33 from its wild homolog SpW […]

call_split

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae

2018
Front Microbiol
PMCID: 5917014
PMID: 29725322
DOI: 10.3389/fmicb.2018.00752
call_split See protocol

[…] eraged prior to hierarchical clustering of the viral gene expression. Figure summarizing this data was constructed using BRIG software (). The putative early promoter motif of AaV was detected using MEME () in discriminative mode. The E-values associated with the discovered motifs are a conservative estimate of the number of motifs having equal or higher log-likelihood ratio if the target sequenc […]


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

MEME review

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Arup Ghosh

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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.