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Genome Biol. 2004;5(7):R50. Epub 2004 Jun 24.

Detecting DNA regulatory motifs by incorporating positional trends in information content.

Author information

  • 1Department of Statistics, University of California, Berkeley, CA 94720, USA. kechris@genome.ucsf.edu

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.

PMID:
15239835
[PubMed - indexed for MEDLINE]
PMCID:
PMC463320
Free PMC Article

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