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Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

Andra Ivan1, Marc S Halfon23 and Saurabh Sinha1*

Author Affiliations

1 Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, N. Goodwin Ave, Urbana, IL 61801, USA

2 Department of Biochemistry, State University of New York at Buffalo, Main St, Buffalo, NY 14214, USA

3 New York State Center of Excellence in Bioinformatics and the Life Sciences, Ellicott St, Buffalo, NY 14203, USA

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Genome Biology 2008, 9:R22  doi:10.1186/gb-2008-9-1-r22

Published: 28 January 2008


We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal.