PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

ABSTRACT: A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we pres

SUBMITTER: Siddharthan R 

PROVIDER: S-EPMC1309704 | biostudies-literature | 2005 Dec

REPOSITORIES: biostudies-literature