Multiple-sequence functional annotation and the generalized hidden Markov phylogeny

Jon D. McAuliffe, Lior Pachter, Michael I. Jordan

Abstract: Phylogenetic shadowing is a comparative genomics principle that allows for the discovery of conserved regions in sequences from multiple closely related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints.