Reference: Kechris KJ, et al. (2004) Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol 5(7):R50

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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.

Reference Type
Comparative Study | Journal Article | Research Support, Non-U.S. Gov't | Research Support, U.S. Gov't, Non-P.H.S. | Research Support, U.S. Gov't, P.H.S.
Authors
Kechris KJ, van Zwet E, Bickel PJ, Eisen MB
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