title: Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes.
abstract: We developed a statistical method that allows each trinucleotide to be associated with a unique frame among the three possible ones in a (protein coding) gene. An extensive gene study in 175 complete bacterial genomes based on this statistical approach resulted in identification of 72 new circular codes. Finding a circular code enables an immediate retrieval of the reading frame locally anywhere in a gene. No knowledge of location of the start codon is required and a short window of only a few nucleotides is sufficient for automatic retrieval. We have therefore developed a factorization method (that explores previously found circular codes) for retrieving the reading frames of bacterial genes. Its principle is new and easy to understand. Neither complex treatment nor specific information on the nucleotide sequences is necessary. Moreover, the method can be used for short regions in nucleotide sequences (less than 25 nucleotides in protein coding genes). Selected additional properties of circular codes and their possible biological consequences are also discussed.
authors.affiliation: Equipe de Bioinformatique Théorique, LSIIT (UMR CNRS-ULP 7005), Université Louis Pasteur de Strasbourg, Pôle API, Boulevard Sébastien Brant, 67400 Illkirch, France. frey@dpt-info.u-strasbg.fr
authors.forename: Gabriel
authors.initials: G
authors.lastname: Frey
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000706:statistics & numerical data*; D008957:Models, Genetic; D015233:Models, Statistical; D016364:Reading Frames