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Nucleic Acids Research Advance Access published online on May 20, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp335
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

MEME SUITE: tools for motif discovery and searching

Timothy L. Bailey1,*, Mikael Boden1, Fabian A. Buske1, Martin Frith2, Charles E. Grant3, Luca Clementi4, Jingyuan Ren4, Wilfred W. Li4 and William S. Noble3,5,*

1Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia, 2Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo, Japan, 3Department of Genome Sciences, University of Washington, Seattle, Washington, 4National Biomedical Computation Resource, University of California, San Diego and 5Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA

*To whom correspondence should be addressed. Tel: 61 7 3346 2614; Fax: 61 7 3346 2103; Email: t.bailey{at}imb.uq.edu.au Correspondence may also be addressed to William S. Noble. Tel: +1 206 543 8930; Fax: +1 206 685 7301; Email: william-noble{at}u.washington.edu

Received February 10, 2009. Revised April 10, 2009. Accepted April 21, 2009.

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and GLAM2SCAN—allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.


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