p-Adic numbers in bioinformatics: from genetic code to PAM-matrix

Abstract

In this paper we denonstrate that the use of the system of 2-adic numbers provides a new insight to some problems of genetics, in particular, generacy of the genetic code and the structure of the PAM matrix in bioinformatics. The 2-adic distance is an ultrametric and applications of ultrametrics in bioinformatics are not surprising. However, by using the 2-adic numbers we match ultrametric with a number theoretic structure. In this way we find new applications of an ultrametric which differ from known up to now in bioinformatics.We obtain the following results. We show that the PAM matrix A allows the expansion into the sum of the two matrices A = A (2) + A (∞) , where the matrix A (2) is 2-adically regular (i.e. matrix elements of this matrix are close to locally constant with respect to the discussed earlier by the authors 2-adic parametrization of the genetic code), and the matrix A (∞) is sparse. We discuss the structure of the matrix A (∞) in relation to the side chain properties of the corresponding amino acids.

Genetic code and number theory

“…As one of the main results that we have obtained is explanation of the structure of the genetic code degeneracy using p-adic distance between codons. A similar approach to the genetic code was later [22], and recently [23] 2-adic distance was applied to the PAM matrix in bioinformatics.…”