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Nucleic Acids Research Advance Access published online on November 27, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl839
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© 2006 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.

Methods Online

CoMoDis: composite motif discovery in mammalian genomes

Ian J. Donaldson* and Berthold Göttgens

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge Hills Road, Cambridge CB2 2XY, UK

*To whom correspondence should be addressed. Tel: +44 161 275 5980; Fax: +44 161 275 5082; Email: ian.donaldson{at}manchester.ac.uk

Received August 17, 2006. Revised October 5, 2006. Accepted October 6, 2006.

Specificity of mammalian gene regulatory regions is achieved to a large extent through the combinatorial binding of sets of transcription factors to distinct binding sites, discrete combinations of which are often referred to as regulatory modules. Identification and subsequent characterization of gene regulatory modules will be a key step in assembling transcriptional regulatory networks from gene expression profiling data, with the ultimate goal of unravelling the regulatory codes that govern gene expression in various cell types. Here we describe the new bioinformatics tool, Composite Motif Discovery (CoMoDis), which streamlines computational identification of novel regulatory modules starting from a single seed motif. Seed motifs represent binding sites conserved across mammalian species. CoMoDis facilitates novel motif discovery by automating the extraction of DNA sequences flanking seed motifs and streamlining downstream motif discovery using a variety of tools, including several that utilize phylogenetic conservation criteria. CoMoDis is available at http://hscl.cimr.cam.ac.uk/CoMoDis_portal.html.

Present address: Ian J. Donaldson, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK


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