I Holmes1. 1. Department of Statistics, University of Oxford. 1 South Parks Road, Oxford OX1 3TG, UK.
Abstract
MOTIVATION: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree. METHODS: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM. RESULTS: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.
MOTIVATION: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree. METHODS: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM. RESULTS: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.
Authors: Benedict Paten; Javier Herrero; Stephen Fitzgerald; Kathryn Beal; Paul Flicek; Ian Holmes; Ewan Birney Journal: Genome Res Date: 2008-10-10 Impact factor: 9.043
Authors: Kemal Sonmez; Naunihal T Zaveri; Ilan A Kerman; Sharon Burke; Charles R Neal; Xinmin Xie; Stanley J Watson; Lawrence Toll Journal: PLoS Comput Biol Date: 2009-01-09 Impact factor: 4.475
Authors: Robert K Bradley; Adam Roberts; Michael Smoot; Sudeep Juvekar; Jaeyoung Do; Colin Dewey; Ian Holmes; Lior Pachter Journal: PLoS Comput Biol Date: 2009-05-29 Impact factor: 4.475