Degrees of divergence in the E. coli genome from correlations between dinucleotide, trinucleotide and codon frequencies

Journal of Biomolecular Structure & Dynamics
P W Hinds, R D Blake

Abstract

Oligonucleotide and codon frequencies have been determined in published sequences of E. coli DNA totaling 103,100bp with 18,459 reading frame trinucleotides; corresponding to 2.5% of the total genome. Dinucleotide frequencies are in excellent agreement with those determined by nearest neighbor chemical analysis, indicating the computer count of a limited sampling to be a good representation of the overall frequencies in total genomic DNA. The distinctive nonrandom codon pattern is found to be uniformly distributed and contributes to a distinctive nonrandom oligonucleotide pattern; enabling correlations between frequency levels to be extended beyond reading frame sequences. Correlation analysis indicates a surprisingly high degree of correlation everywhere in the genome. Coefficients of correlation between oligonucleotide frequencies overall and those in specific segments vary as follows: primary strands of individual coding sequences greater than 0.9 greater than lambda DNA greater than noncoding, non-RNA greater than phi X174 DNA greater than complementary strands greater than RNA genes congruent to 0.6 greater than transposon-insertion elements greater than T7DNA much greater than eukaryotic sequences congruent to 0. It is co...Continue Reading

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Citations

Mar 1, 1992·Journal of Molecular Evolution·R D BlakeJ Nicholson-Tuell
Jan 1, 1986·Progress in Biophysics and Molecular Biology·A Wada, A Suyama
Jul 1, 1987·Biopolymers·R D Blake
Dec 1, 1984·Journal of Biomolecular Structure & Dynamics·R D Blake, P W Hinds
Oct 1, 1986·Journal of Biomolecular Structure & Dynamics·R D Blake, S Earley
Feb 1, 1986·Journal of Biomolecular Structure & Dynamics·A S Kolaskar, B V Reddy
Feb 22, 1989·Journal of Theoretical Biology·P R SibbaldJ Maze

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