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Codon information value and codon transition-probability distributions in short-term evolution. (English) Zbl 1400.92397
Summary: To understand the way the Genetic Code and the physical-chemical properties of coded amino acids affect accepted amino acid substitutions in short-term protein evolution, taking into account only overall amino acid conservation, we consider an underlying codon-level model. This model employs codon pair-substitution frequencies from an empirical matrix in the literature, modified for single-base mutations only. Ordering the degenerated codons according to their codon information value [M. Volkenstein, “Mutations and the value of information”, J. Theoret. Biol. 80, No. 2, 155–169 (1979; doi:10.1016/0022-5193(79)90202-9)], we found that three-fold and most of four-fold degenerated codons, which have low codon values, were best fitted to rank-frequency distributions with constant failure rate (exponentials). In contrast, almost all two-fold degenerated codons, which have high codon values, were best fitted to rank-frequency distributions with variable failure rate (inverse power-laws). Six-fold degenerated codons are considered to be doubly assigned. The exceptional behavior of some codons, including non-degenerate codons, is discussed.
Reviewer: Reviewer (Berlin)
MSC:
92D20 Protein sequences, DNA sequences
Software:
ROOT
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