title: Computer System for Analysis of Molecular Evolution Modes (SAMEM): analysis of molecular evolution modes at deep inner branches of the phylogenetic tree.
abstract: SAMEM (System for Analysis of Molecular Evolution Modes), a web-based pipeline system for inferring modes of molecular evolution in genes and proteins (http://pixie.bionet.nsc.ru/samem/), is presented. Pipeline 1 performs analyses of protein-coding gene evolution; pipeline 2 performs analyses of protein evolution; pipeline 3 prepares datasets of genes and/or proteins, performs their primary analysis, and builds BLOSUM matrices; pipeline 4 checks if these genes really are protein-coding. Pipeline 1 has an all-new feature, which allows the user to obtain K(R)/K(C) estimates using several different methods. An important feature of pipeline 2 is an original method for analyzing the rates of amino acid substitutions at the branches of a phylogenetic tree. The method is based on Markov modeling and a non-parametric permutation test, which compares expected and observed frequencies of amino acid substitutions, and infers the modes of molecular evolution at deep inner branches.
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. genkvg@gmail.com
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Gunbin
authors.forename: Valentin V
authors.initials: VV
authors.lastname: Suslov
authors.forename: Mikhail A
authors.initials: MA
authors.lastname: Genaev
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Afonnikov
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000235:genetics; D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D008390:Markov Chains; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins