title: A generalization of substitution evolution models of nucleotides to genetic motifs.
abstract: We generalize here the classical stochastic substitution models of nucleotides to genetic motifs of any size. This generalized model gives the analytical occurrence probabilities of genetic motifs as a function of a substitution matrix containing up to three formal parameters (substitution rates) per motif site and of an initial occurrence probability vector of genetic motifs. The evolution direction can be direct (past-present) or inverse (present-past). This extension has been made due to the identification of a Kronecker relation between the nucleotide substitution matrices and the motif substitution matrices. The evolution models for motifs of size 4 (tetranucleotides) and 5 (pentanucleotides) are now included in the SEGM (Stochastic Evolution of Genetic Motifs) web server.
authors.affiliation: Equipe de Bioinformatique Théorique, FDBT, LSIIT (UMR 7005), Université de Strasbourg, Pôle API, Boulevard Sébastien Brant, 67400 Illkirch, France. benard@dpt-info.u-strasbg.fr
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Benard
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020407:Internet; D008957:Models, Genetic; D059372:Nucleotide Motifs / Q000235:genetics*; D012984:Software; D013269:Stochastic Processes