title: Translation conditional models for protein coding sequences.
abstract: A coding sequence is defined as a DNA sequence coding the primary structure of a protein (a polypeptide). Such a sequence must satisfy a specific constraint, which consists in coding a functional protein. As the genetic code is degenerated, there exists, for a given polypeptide, a set of synonymous sequences which would code the same polypeptide. Translation conditional models are being defined on such sets. The aim of this paper is to give a common formalism. Besides the codon bias model, a few other conditional models will be defined. Statistical estimators and comparison methods will be briefly presented. These models can be used for gene classification, or to find out, in a real sequence, remarkable features. An example will be presented on Escherichia coli genes.
authors.affiliation: INRA, Unité MIG, Jouy en Josas, France. fr@jouy.inra.fr
authors.forename: F
authors.initials: F
authors.lastname: Rodolphe
authors.forename: C
authors.initials: C
authors.lastname: Mathé
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001699:Biometry; D003062:Codon / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D005798:Genes, Bacterial; D008390:Markov Chains; D008957:Models, Genetic; D014176:Protein Biosynthesis; D011506:Proteins / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D004269:DNA, Bacterial; D011506:Proteins