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Genome Biol. 2004;5(12):R98. Epub 2004 Nov 30.

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

Author information

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

Abstract

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

PMID:
15575972
PMCID:
PMC545801
DOI:
10.1186/gb-2004-5-12-r98
[PubMed - indexed for MEDLINE]
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