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

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...

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Detalles Bibliográficos
Autores principales: Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2004
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545801/
https://www.ncbi.nlm.nih.gov/pubmed/15575972
http://dx.doi.org/10.1186/gb-2004-5-12-r98
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author Moses, Alan M
Chiang, Derek Y
Pollard, Daniel A
Iyer, Venky N
Eisen, Michael B
author_facet Moses, Alan M
Chiang, Derek Y
Pollard, Daniel A
Iyer, Venky N
Eisen, Michael B
author_sort Moses, Alan M
collection PubMed
description 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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spelling pubmed-5458012005-01-27 MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model Moses, Alan M Chiang, Derek Y Pollard, Daniel A Iyer, Venky N Eisen, Michael B Genome Biol Method 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. BioMed Central 2004 2004-11-30 /pmc/articles/PMC545801/ /pubmed/15575972 http://dx.doi.org/10.1186/gb-2004-5-12-r98 Text en Copyright © 2004 Moses et al; licensee BioMed Central Ltd.
spellingShingle Method
Moses, Alan M
Chiang, Derek Y
Pollard, Daniel A
Iyer, Venky N
Eisen, Michael B
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title_full MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title_fullStr MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title_full_unstemmed MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title_short MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
title_sort monkey: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545801/
https://www.ncbi.nlm.nih.gov/pubmed/15575972
http://dx.doi.org/10.1186/gb-2004-5-12-r98
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