PhyloGibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms. Many existing approaches to either search for sequence-motifs that are overrepresented in the input data, or for sequence-segments that are more conserved evolutionary than expected. PhyloGibbs combines these two approaches and identifies significant sequence-motifs by taking both over-representation and conservation signals into account.
PhyloGibbs-MP is a significant enhancement.
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Rahul Siddharthan, Eric D. Siggia, and Erik van Nimwegen
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
PLoS Comput Biol 1(7): e67 2005