MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

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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.

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Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN. & Eisen, Michael B. October 28, 2004.

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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.

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  • Journal Name: Genome Biology; Journal Volume: 5; Journal Issue: 12; Related Information: Journal Publication Date: 11/30/2004

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  • Report No.: LBNL--58111
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: NIHR1HG002779A
  • Office of Scientific & Technical Information Report Number: 860794
  • Archival Resource Key: ark:/67531/metadc778685

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  • October 28, 2004

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  • Dec. 3, 2015, 9:30 a.m.

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  • April 1, 2016, 8:17 p.m.

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Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN. & Eisen, Michael B. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel, article, October 28, 2004; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc778685/: accessed November 18, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.