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MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific

Alan M Moses1, Derek Y Chiang, Daniel A Pollard

  • 1Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA. amoses@berkeley.edu <amoses@berkeley.edu>

Genome Biology
|December 4, 2004
PubMed
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We developed MONKEY, a novel method to find conserved transcription-factor binding sites in multiple species. This tool uses probabilistic models to assess the evolutionary conservation and statistical significance of potential binding sites.

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Identifying conserved transcription-factor binding sites (TFBS) is crucial for understanding gene regulation.
  • Evolutionary conservation can indicate functional importance of regulatory elements.

Purpose of the Study:

  • To introduce a new computational method, MONKEY, for identifying conserved TFBS across multiple species.
  • To evaluate the method's performance using yeast genomes and explore the link between conservation and function.

Main Methods:

  • Development of MONKEY, a method utilizing probabilistic models of transcription factor specificity and binding-site evolution.
  • Computation of conservation likelihood and statistical significance for putative TFBS in multispecies alignments.
  • Application to genomes from the Saccharomyces genus.

Related Experiment Videos

Main Results:

  • MONKEY successfully identifies conserved TFBS in multispecies alignments.
  • The statistical significance of real TFBS increases with evolutionary distance in Saccharomyces genomes.
  • Demonstration of a relationship between the conservation of TFBS and their functional relevance.

Conclusions:

  • MONKEY provides a robust approach for discovering conserved regulatory elements.
  • Evolutionary distance is a key factor in assessing the significance of TFBS conservation.
  • The study highlights the utility of comparative genomics for functional inference of regulatory sites.