Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
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
Genome Biology 2008, 9:R22 doi:10.1186/gb-2008-9-1-r22Published: 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.