Work

Detecting DNA regulatory motifs by incorporating positional trends in information content

Year: 2004

Type: article

Abstract: On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

Source: Genome biology

DOI: 10.1186/gb-2004-5-7-r50

Authors: Katherina J Kechris, Erik van Zwet, Peter J Bickel, Michael B Eisen

Institutions: University of California, San Francisco, University of California, Berkeley, Lawrence Berkeley National Laboratory

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 Science Foundation, National Institutes of Health, National Human Genome Research Institute