MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
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ABSTRACT:
SUBMITTER: Moses AM
PROVIDER: S-EPMC545801 | biostudies-other | 2004
REPOSITORIES: biostudies-other
Publications
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Moses Alan M AM Chiang Derek Y DY Pollard Daniel A DA Iyer Venky N VN Eisen Michael B MB
Genome biology 20041130 12
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 conserv ...[more]
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