title: An analytical model of gene evolution with 9 mutation parameters: an application to the amino acids coded by the common circular code.
abstract: We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code [Formula: see text] of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code [Formula: see text] is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by [Formula: see text] has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code [Formula: see text] and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.
authors.affiliation: Equipe de Bioinformatique Théorique, LSIIT (UMR CNRS-ULP 7005), Université Louis Pasteur de Strasbourg, Pôle API, Boulevard Sébastien Brant, 67400 Illkirch, France. michel@dpt-info.u-strasbg.fr
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D005057:Eukaryotic Cells; D019143:Evolution, Molecular; D008957:Models, Genetic; D011387:Prokaryotic Cells
chemical_list: D000596:Amino Acids; D003062:Codon