Method

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

Alan M Moses^1,2 , Derek Y Chiang³ , Daniel A Pollard¹ , Venky N Iyer⁴ and Michael B Eisen^2,3,4

¹  Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA

²  Center for Integrative Genomics, University of California, Berkeley, CA 94720

³  Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA

⁴  Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, 1 Cyclotron Road, CA 942770, USA

author email corresponding author email

Genome Biology 2004, 5:R98doi:10.1186/gb-2004-5-12-r98

Published:	30 November 2004

Subject areas: Bioinformatics, Evolution, Genome studies

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.