Additional excerpts

Toward in Silico Biology (from Sequences to Systems)

2-Adic clustering of the PAM matrix.

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^{(\infty)}, 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^{(\infty)} is sparse. We discuss the structure of the matrix A^{(\infty)} in relation to the side chain properties of the corresponding amino acids.

background

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

Preface The Enteric Bacterial Cell and the Age of Bacteria Variations on a Theme by Escherichia Part I: Molecular Architecture and Assembly of Cell Parts (11 chapters) Part II: Metabolism and General Physiology (58 chapters) Part III: Utilization of Energy for Cell Activities (7 chapters) Part IV: Regulation of Gene Expression (19 chapters) Part V: Growth of Cells and Cultures (12 chapters) Part VI: Genome, Genetics and Evolution (40 chapters) Part VII: Molecular Pathogenesis (7 chapters)

Toward in Silico Biology (from Sequences to Systems)

Citations

2-Adic clustering of the PAM matrix.

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

References

Escherichia coli and Salmonella :cellular and molecular biology

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