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  • Title: Representation of mutation pressure and selection pressure by PAM matrices.
    Author: Nowicka A, Mackiewicz P, Dudkiewicz M, Mackiewicz D, Kowalczuk M, Banaszak J, Cebrat S, Dudek MR.
    Journal: Appl Bioinformatics; 2004; 3(1):31-9. PubMed ID: 16323964.
    Abstract:
    This paper analyses the relationship between the mutation data matrix 1PAM/PET91, representing the effect of both mutation and selection pressures exerted on 16130 homologous proteins of different organisms, and a mutation probability matrix (1PAM/MPM) representing the effect of pure mutation pressure on protein coding of the Borrelia burgdorferi genome. The 1PAM/PMP matrix was derived with the help of computer simulations, which used empirical nucleotide substitution rates found for the B. burgdorferi genome. Here, it is shown that the frequency of amino acid occurrence is strongly related to their effective survival time. We found that the shorter the turnover time of an amino acid under pure mutation pressure, the lower its fraction in the proteins coded by the genome and the more protected by selection pressure is its position in proteins. Results of analyses suggest that during evolution the mutational pressure has been optimised to some extent to the selection requirements.
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