A New Phylo-HMM Paradigm to Search for Sequences

Abstract : We introduce a new type of phylogenetic Hidden Markov Model, combining the strength of usual HMM and the knowledge of the phylogeny of a family of sequences. We use such models to look into the genome of a target species for members of the sequence family. Our results on some 690 protein families show a better sensitivity and a better specificity when compared to standard profile HMM or Blast searchs.