Russian Journal of Biological Physics and Chemisrty Russian Journal of Biological Physics and Chemisrty АКТУАЛЬНЫЕ ВОПРОСЫ БИОЛОГИЧЕСКОЙ ФИЗИКИ И ХИМИИ 2499-9962 83706 10.29039/rusjbpc.2023.0640 МОДЕЛИРОВАНИЕ В БИОФИЗИКЕ И БИОИНФОРМАТИКА MODELLING IN BIOPHYCIS AND BIOINFORMATISC МОДЕЛИРОВАНИЕ В БИОФИЗИКЕ И БИОИНФОРМАТИКА COMPUTATIONAL TOOLS FOR THE DNA TEXT COMPLEXITY ESTIMATES FOR MICROBIAL GENOMES STRUCTURE ANALYSIS КОМПЬЮТЕРНЫЕ ПРОГРАММЫ ОЦЕНКИ СЛОЖНОСТИ ТЕКСТА ДНК ДЛЯ АНАЛИЗА СТРУКТУРЫ ГЕНОМОВ МИКРООРГАНИЗМОВ Митина А. В. Mitina A. V. Орлова Н. Г. Orlova N. G. Дергилев А. И. Dergilev A. I. Орлов Юрий Львович Orlov Yuriy L'vovich orlov@d-health.institute

доктор биологических наук;

doctor of sciences in biology;

 Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Финансовый Университет при Правительстве РФ Москва Россия Financial University under the Government of the Russian Federation Moscow Russian Federation Новосибирский государственный университет Новосибирск Россия Novosibirsk State University Novosibirsk Russian Federation Институт цитологии и генетики СО РАН Новосибирск Россия Institute of Cytology and Genetics SB RAS Novosibirsk Russian Federation Первый МГМУ им. И.М. Сеченова Минздрава России (Сеченовский Университет) Москва Россия Sechenov University Moscow Russian Federation Институт цитологии и генетики СО РАН Новосибирск Россия Institute of Cytology and Genetics SB RAS Novosibirsk Russian Federation Новосибирский государственный университет Новосибирск Россия Novosibirsk State University Novosibirsk Russian Federation Российский университет дружбы народов Peoples’ Friendship University of Russia 06 06 2024 06 06 2024 8 4 408 416 02 08 2023 https://rusjbpc.ru/en/nauka/article/83706/view

Одна из классических задач биоинформатики - поиск повторов и статистически неоднородных участков последовательностей ДНК и полных геномов микроорганизмов. Теоретические подходы к исследованию сложности текста последовательностей макромолекул - ДНК, РНК и белков – развивались до появления полных геномных последовательностей и получили новый импульс в связи с распространением технологий массового параллельного секвенирования и бурным ростом доступных данных. Рассматриваются современные компьютерные методы и существующие программы оценки сложности текста ДНК и построения профиля свойств для анализа структуры геномов микроорганизмов. Дан обзор доступных онлайн-программ для поиска и визуализации повторов текста. Представлена собственная компьютерная реализация метода оценки лингвистической сложности текста и сжатия по Лемпелю-Зиву для выявления структурных особенностей и аномалий геномов микроорганизмов. Представлены примеры профилей анализа сложности текста. Рассмотрено применение оценок сложности к анализу последовательности генома коронавируса SARS-CoV2, последовательности вируса эндемического паротита Mumps Orthorubulavirus. Выявлены участки низкой сложности текста.

One of the fundamental tasks in bioinformatics involves searching for repeats, which are statistically heterogeneous segments within DNA sequences and complete genomes of microorganisms. Theoretical approaches to analyzing the complexity of macromolecule sequences (DNA, RNA, and proteins) were established prior to the availability of complete genomic sequences. These approaches have experienced a resurgence due to the proliferation of mass parallel sequencing technologies and the exponential growth of accessible data. This article explores contemporary computer methods and existing programs designed to assess DNA text complexity as well as construct profiles of properties for analysing the genomic structures of microorganisms. The article offers a comprehensive overview of available online programs designed for detecting and visualising repeats within genetic text. Furthermore, the paper introduces a novel computer-based implementation of a method to evaluate the linguistic complexity of text and its compression using Lempel-Ziv. This approach aims to identify structural features and anomalies within the genomes of microorganisms. The article also provides examples of profiles generated through the analysis of text complexity. Application of these complexity estimates in the analysis of genome sequences, such as those of the SARS-CoV-2 coronavirus and the Mumps Orthorubulavirus, is discussed. Specific areas of low complexity within the genetic text have been successfully identified in this research.

 биоинформатика биофизические модели сложность текста геномы микроорганизмов bioinformatics biophysical models text complexity microbial genomes Работа поддержана грантом РНФ (23-44-00030).

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