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Bioinformatics Advance Access published online on June 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm299
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Finding Cis-Regulatory Modules in Drosophila using Phylogenetic Hidden Markov Models

Wendy S.W. Wong 1,2,* and Rasmus Nielsen 3

1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
2Department of Biology and Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh ø, Denmark
3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

*To whom correspondence should be addressed. Ms. S. W. Wendy Wong, E-mail: sww8{at}cornell.edu


  Abstract

Motivation: Finding the regulatory modules for transcription factors binding is an important step in elucidating the complex molecular mechanisms underlying regulation of gene expression. There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data.

Results: We develop a method for finding regulatory modules in Eukaryotic species using phylogenetic data. Using computer simulations and analysis of real data, we show that the use of phylogenetic hidden Markov model can lead to an increase in accuracy of prediction over methods that do not take advantage of the data from multiple species.

Availability: The new method is made accessible under GPL in a new publicly available JAVA program: EvoPromoter. It can be downloaded at http://sourceforge.net/projects/evopromoter/.

Associate Editor: Dr. Alex Bateman

Received on November 1, 2006; revised on May 28, 2007; accepted on May 29, 2007

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