Method

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

Andra Ivan¹ , Marc S Halfon^2,3 and Saurabh Sinha¹

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

author email corresponding author email

Genome Biology 2008, 9:R22doi:10.1186/gb-2008-9-1-r22

Published:	28 January 2008

Subject areas: Bioinformatics, Methods

Abstract

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.