Study of a perturbation in the coding periodicity

DOI10.1016/0025-5564(87)90060-5MaRDI QIDQ579160zbMATH OpenOpenAlexFDO

Authors Didier G. Arquès, Christian J. Michel

Publication date 1987

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/0025-5564(87)90060-5

zbMATH Keywords

biochemistrychloroplastscoding periodicitydinucleotideeukaryotesgene taxonomic groupsmean curvesmitochondriamodulo 3 periodicitymodulo 9 periodicitynucleotide sequenceoccurrence probabilityprincipal component analysesprotein coding genespurine basepyrimidine basespatial structure of the DNA sequencestransfer RNA genestrinucleotide

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Physiological, cellular and medical topics (92Cxx)

Review text

The statistical study of different populations of genes, with principal component analyses (PCA) and with mean curves, shows: (1) The occurrence probability of the dinucleotide \(D=RY\) \((D'=YR)\), R being a purine base, Y a pyrimidine base, and N any base, after the occurrence of the nucleotide Y(R) in the zero modulo three curve - in the eukaryotic protein coding genes - presents a modulo 9 periodicity with a maximum value nine bases after Y(R). This modulo 9 periodicity is added to the existing coding modulo 3 periodicity RNY, i.e. to the preferential use of the codon RNY in the open reading frame. (2) The occurrence probability of the trinucleotide \(T=YRY\) after the occurrence of the nucleotide Y - in the protein coding genes of eukaryotes, chloroplasts, and mitochondria and in the transfer RNA genes - presents a maximum value eight bases after Y. (3) Similar results are obtained (with less statistical significance) with other gene taxonomic groups (viral protein coding genes, viral introns) and with the complementary motif \(R(N)_ 8RYR.\) These results may suggest that the motifs \(Y(N)_ 8YRY\), \(R(N)_ 8RYR\), \(Y(N)_ 9RY\), and \(R(N)_ 9YR\) could have a function related to the spatial structure of the DNA sequences.

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Cited in

(9)

• A study of the purine/pyrimidine codon occurrence with a reduced centered variable and an evaluation compared to the frequency statistic
• Analytical expression of the purine-pyrimidine codon probability after and before random mutations
• Analytical expression of the purine/pyrimidine autocorrelation function after and before random mutations
• How to choose biomarkers in view of parameter estimation
• Statistics of trinucleotides in coding sequences and evolution
• Study of triplet periodicity differences inside and between genomes
• Characterization of base periodicities in protein-coding genes
• Stochastic model of homogeneous coding and latent periodicity in DNA sequences
• A model of DNA sequence evolution

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