Codon preference and primary sequence structure in protein-coding regions

DOI10.1007/BF02458838MaRDI QIDQ1111970zbMATH OpenOpenAlexWikidataFDO

Authors Simon Tavaré, Brenda Song

Publication date 1989

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/bf02458838

zbMATH Keywords

codon preferencedata base of 365 protein-coding regionsestimation of species phylogenymolecular biologynon- homogeneous modelspatially homogeneous Markov sourcestochastic complexitysubstitution rates

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Physiological, cellular and medical topics (92Cxx) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Review text

The stochastic complexity of a data base of 365 protein-coding regions is analysed. When the primary sequence is modeled as a spatially homogeneous Markov source, the fit to observed codon preference is very poor. The situation improves substantially when a non-homogeneous model is used. Some implications for the estimation of species phylogeny and substitution rates are discussed.

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Cites work

• A measure of the similarity of sets of sequences not requiring sequence alignment.
• A search for patterns in the nucleotide sequence of the MS2 genome
• Determination of the order of a Markov chain by Akaike's information criterion
• scientific article; zbMATH DE number 3174032 (Why is no real title available?)
• On Some Criteria for Estimating the Order of a Markov Chain
• Statistical Inference of Phylogenies

Cited in

(8)

• Comparative statistical analysis of bacteria genomes in ``word context
• Natural distinct inter-preference between genetic codon and protein secondary structure combinations
• Codon and amino-acid distribution in DNA
• In-phase implies large likelihood for independent codon model: distinguishing coding from non-coding sequences
• The positive selection estimated by a codon substitution model with codon usage bias
• CODON DISTRIBUTIONS IN DNA SEQUENCE OF ESCHERICHIA COLI
• Visualizing codon usage within and across genomes: concepts and tools
• Uniform accuracy of the maximum likelihood estimates for probabilistic models of biological sequences

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