Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, N, Goodwin Ave, Urbana, IL 61801, USA. sinhas@cs.uiuc.edu.
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.