Translation conditional models for protein coding sequences

J Comput Biol. 2000 Feb-Apr;7(1-2):249-60. doi: 10.1089/10665270050081504.

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.

Publication types

  • Comparative Study

MeSH terms

  • Bacterial Proteins / genetics
  • Base Sequence
  • Biometry
  • Codon / genetics
  • DNA, Bacterial / genetics
  • Escherichia coli / genetics
  • Genes, Bacterial
  • Markov Chains
  • Models, Genetic*
  • Protein Biosynthesis*
  • Proteins / genetics*

Substances

  • Bacterial Proteins
  • Codon
  • DNA, Bacterial
  • Proteins