Detecting DNA regulatory motifs by incorporating positional trends in information content
Open Access
- 24 June 2004
- journal article
- research article
- Published by Springer Nature in Genome Biology
- Vol. 5 (7) , R50
- https://doi.org/10.1186/gb-2004-5-7-r50
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.Keywords
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