An approach to analysis of the similarity of DNA-sequences

Abstract

This paper describes algorithms, corresponding computer programs and the results of computations, supplementing results published earlier. We consider the multiple sequence alignment problem, which can be nominated by a central problem in computational biology. For it, we continue to consider some different versions of so-called “triangular norm” defined on the set of triangles formed by the different distance between genomes computed by different algorithms. Besides, one of the problems considered in biocybernetics is the problem of reconstructing the distance matrix between DNA sequences, when not all the elements of the matrix under consideration are known at the input of the algorithm. In this connection, the problem arises that the developed method of comparative evaluation of algorithms for calculating the distances between sequences should be used for another problem, i.e., for reconstructing the matrix of distances between DNA sequences. In this paper, we consider the possibility of applying the method of comparative evaluation of the algorithms for calculating the distances between a pair of DNA strings that we developed and studied earlier for the reconstruction of a partially filled distance matrix. The restoration of the matrix occurs as a result of several computational passes. Estimates of unknown matrix elements are averaged in a special way using so-called risk functions, and the result of this averaging is considered as the received value of the unknown element.