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. 2015 Jul 1;43(W1):W39-49.
doi: 10.1093/nar/gkv416. Epub 2015 May 7.

The MEME Suite

Timothy L Bailey  1 , James Johnson  2 , Charles E Grant  3 , William S Noble  4
Affiliations

The MEME Suite

Timothy L Bailey et al. Nucleic Acids Res. .

Abstract

The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression. Since the previous description of the MEME Suite in the 2009 Nucleic Acids Research Web Server Issue, we have added six new tools. Here we describe the capabilities of all the tools within the suite, give advice on their best use and provide several case studies to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses. The MEME Suite is freely available for academic use at http://meme-suite.org, and source code is also available for download and local installation.

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Figures

Figure 1.
Figure 1.
Overview of the integrated tools in the MEME Suite. Tools added since the MEME Suite web server was last described (15) are underlined.
Figure 2.
Figure 2.
fimo input form showing interactive display of motif logo for typed in motifs.
Figure 3.
Figure 3.
Secretory signal in P. falciparum proteins discovered using meme and mast. (A) The logo of the motif discovered by meme in the N-terminal regions of of five proteins known to be secreted by P. falciparum. (B) The logo of the motif discovered by meme in the 150 aa N-terminal regions of 184 proteins where fimo reports a match to the first motif. (C) A portion of the mast ‘Block Diagram’ output illustrating the relative positions of matches to the first motif.
Figure 4.
Figure 4.
Discovery of CENP-T motif involved in interacting with Ndc80. (A) The locations of the three discovered motifs within the 31 CENP-T homologs. The figure includes non-overlapping sites with a P-value better than 0.0001. The height of the motif ‘block’ is proportional to −log (P-value), truncated at the height for a motif with a P-value of 10−10. (B) The third motif found by meme in CENP-T homologs.
Figure 5.
Figure 5.
Using mcast to predict CRMs near CYP3A4 and CYP3A5. The figure shows nine mcast-predicted CRMs alongside five experimental tracks: three ChIP-seq experiments for liver-specific factors PPARGC1A, CEBP and HNF4α, and two DNaseI sensitivity analyses. The best-scoring CRM is boxed in green. The DNaseI experiments are illustrated both as signal tracks and as a combined set of peak calls. Various isoforms of several CYP3A genes are shown, as well as a portion of the gene ZSCAN25.
Figure 6.
Figure 6.
meme-Chip analysis of VDR Chip-seq data. (A) Tomtom alignment of the JASPAR motif for VDR (top) and the first motif discovered by meme (bottom). (B) CentriMo analysis showing central enrichment of the VDR motif within the given ChIP-seq peaks.
None
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See this image and copyright information in PMC

References

    1. Bailey T.L., Elkan C.P. Fitting a mixture model by expectation-maximization to discover motifs in biopolymers. In: Altman R, Brutlag D, Karp P, Lathrop R, Searls D, editors. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. Menlo Park, CA: AAAI Press; 1994. pp. 28–36. - PubMed
    1. Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994;2:28–36. - PubMed
    1. Bailey T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27:1653–1659. - PMC - PubMed
    1. Machanick P., Bailey T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics. 2011;27:1696–1697. - PMC - PubMed
    1. Frith M.C., Saunders N.F.W., Kobe B., Bailey T.L. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput. Biol. 2008;4:e1000071. - PMC - PubMed

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