PhylCRM is a new cis-regulatory module (CRM) prediction algorithm. PhylCRM combines data for individual motif occurances scored on an alignment using previously described MONKEY scoring sheme (Moses et al., Genome Biology 5, R98, 2004) into a single CRM prediction. PhylCRM can scan very long genomic sequences for candidate CRMs by quantifying both motif clustering and conservation across arbitrarily many genomes using an evolutionary model consistent with the phylogeny of the genomes.
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Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.
Systematic identification of mammalian regulatory motifs’ target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.