MEME suite: Tools for motif discovery and searching

Bailey, T. L., Boden, M. B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J. Y., Li, W. W. and Noble, W. S. (2009) MEME suite: Tools for motif discovery and searching. Nucleic Acids Research, 37 Suppl. 2: W202-W208. doi:10.1093/nar/gkp335

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Author Bailey, T. L.
Boden, M. B.
Buske, F. A.
Frith, M.
Grant, C. E.
Clementi, L.
Ren, J. Y.
Li, W. W.
Noble, W. S.
Title MEME suite: Tools for motif discovery and searching
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
1362-4954
Publication date 2009
Sub-type Article (original research)
DOI 10.1093/nar/gkp335
Open Access Status DOI
Volume 37
Issue Suppl. 2
Start page W202
End page W208
Total pages 7
Editor Fox, K.
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2010
Language eng
Subject C1
89 Information and Communication Services
8902 Computer Software and Services
08 Information and Computing Sciences
080301 Bioinformatics Software
Abstract 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.
Keyword Sequence motifs
Environment
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Created: Thu, 03 Sep 2009, 07:49:56 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience