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

  • Author(s): Kechris, Katherina J.
  • van Zwet, Erik
  • Bickel, Peter J.
  • Eisen, Michael B.
  • et al.
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.

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