Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.
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.
Ivan
Andra
A
Department of Computer Science and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Halfon
Marc S
MS
Sinha
Saurabh
S
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004330:Drosophila / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D017344:Genes, Insect