The Matrix Method of Representation, Analysis and Classification of Long Genetic Sequences

Abstract

Abstract:The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed.

A multiscale model of nucleic acid imaging

“…The above method is an algorithm of computer processing of biological information for scale parametric visualization of nucleic acids in coordinate spaces of different dimensions. The main ideas of this method were first proposed by the author in [5]. The steps of the developed algorithm are given below.…”

Scaling and Visualization of Nucleotide Sequences

“…You can analyze the connectedness matrices corresponding to the graphs, but the absence of pronounced symmetries reflecting the nucleotide composition does not provide a fundamentally new quality. Therefore, for a more informative assessment, we decided to use the considerations developed and presented by us in [6]. These considerations are based on the ideas of semantic visualization (the presence of a free scaling parameter) and taking into account the physicochemical parameters of nucleotides.…”

“…Information on Hadamard symmetries and matrices in genetic coding is studied in detail in the works of S.V. Petukhov in the framework of matrix genetics [5,6,10].…”

“…The presented algorithm is the author's one, was firstly presented at [6] and underlies the reconstruction of a scale-parametric model of the genome for visualization in coordinate spaces of various dimensions and topology.…”

“…1) a sequence of characters from the set {A, G, C, T} or {A, G, C, U} encoding nitrogen bases is divided into fragments of equal length N, where N is a free parameter of the algorithm -the word length. The resulting fragments of equal length will be called N-plets [6];…”