Translation conditional models for protein coding sequences.
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.
Rodolphe
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INRA, Unité MIG, Jouy en Josas, France. fr@jouy.inra.fr
Mathé
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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*
D001426:Bacterial Proteins; D003062:Codon; D004269:DNA, Bacterial; D011506:Proteins