MONKEY swMATH ID: 33139 Software Authors: Alan Moses, Derek Chiang, Daniel Pollard, Venky Iyer, Michael Eisen Description: 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 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. Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545801/ Related Software: GitHub; ThIEF; Galaxy; DGW; Bowtie 2; ChromHMM; modENCODE; PuFFIN; BEDTools; Clustal X; MUSCLE; CLUSTAL; ClustalW; LIBSVM; GLPK Cited in: 1 Document all top 5 Cited by 6 Authors 1 Bunnik, Evelien M. 1 Hasan, Md. Abid 1 Le Roch, Karine 1 Lonardi, Stefano 1 Pan, Weihua 1 Polishko, Anton Cited in 0 Serials Cited in 1 Field 1 Biology and other natural sciences (92-XX) Citations by Year