Work

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

Year: 2008

Type: article

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.

Source: Genome biology

DOI: 10.1186/gb-2008-9-1-r22

Authors: Andra Ivan, Marc S Halfon, Saurabh Sinha

Institutions: University of Illinois Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, University at Buffalo, State University of New York

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: National Institutes of Health, University of Illinois at Urbana-Champaign, National Human Genome Research Institute