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A Markov information source for the syntactic characterization of amino acid substitutions in protein evolution. (English) Zbl 1324.92025

Summary: We introduce a theoretical model, which consists of a Markov information source that generates codon sequences, and from them amino acid sequences, that maintain the same or very similar functions and structures, as a direct consequence of the structure of the genetic code, and general physical chemical constraints. With the help of the model, we propose a codon dendrogram to describe a hierarchy of codon categorizations, which explain the pattern of frequent amino acid substitutions in short term evolution.

MSC:

92D20 Protein sequences, DNA sequences
92C40 Biochemistry, molecular biology
92D15 Problems related to evolution
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