Lawrence Berkeley National Laboratory
Detecting DNA regulatory motifs by incorporating positional trends in information
- Author(s): Kechris, Katherina J.
- van Zwet, Erik
- Bickel, Peter J.
- Eisen, Michael B.
- et al.
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.