Detecting DNA regulatory motifs by incorporating positional trends in information content

Genome Biol. 2004;5(7):R50. doi: 10.1186/gb-2004-5-7-r50. Epub 2004 Jun 24.


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.

Publication types

  • Comparative Study
  • 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.

MeSH terms

  • Algorithms
  • Base Composition / genetics*
  • Computational Biology / statistics & numerical data
  • Computer Simulation
  • DNA, Fungal / genetics*
  • Genes, Fungal / genetics
  • Models, Genetic
  • Prions / genetics
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Saccharomyces cerevisiae / genetics
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, DNA / statistics & numerical data


  • DNA, Fungal
  • Prions