Discriminative Motifs

Research output: Contribution to journalArticlepeer-review


This paper takes a new view of motif discovery, addressing a common problem in existing motif finders. A motif is treated as a feature of the input promoter regions that leads to a good classifier between these promoters and a set of background promoters. This perspective allows us to adapt existing methods of feature selection, a well-studied topic in machine learning, to motif discovery. We develop a general algorithmic framework that can be specialized to work with a wide variety of motif models, including consensus models with degenerate symbols or mismatches, and composite motifs. A key feature of our algorithm is that it measures overrepresentation while maintaining information about the distribution of motif instances in individual promoters. The assessment of a motif's discriminative power is normalized against chance behaviour by a probabilistic analysis. We apply our framework to two popular motif models and are able to detect several known binding sites in sets of co-regulated genes in yeast.

Original languageEnglish (US)
Pages (from-to)599-615
Number of pages17
JournalJournal of Computational Biology
Issue number3-4
StatePublished - 2003
Externally publishedYes


  • Motif finding
  • Overrepresentation
  • TNoM score
  • Transcription factor binding sites

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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