Local Symmetry of Non-Coding Genetic Sequences

Radavičius, Marijus; Rekašius, Tomas; Židanavičiūtė, Jurgita

doi:10.15388/Informatica.2019.218

Informatica

Local Symmetry of Non-Coding Genetic Sequences

Volume 30, Issue 3 (2019), pp. 553–571

Marijus Radavičius Tomas Rekašius Jurgita Židanavičiūtė

https://doi.org/10.15388/Informatica.2019.218

Pub. online: 1 January 2019 Type: Research Article

Open Access

Received
1 November 2018

Accepted
1 May 2019

Published
1 January 2019

Abstract

The simplest hypothesis of DNA strand symmetry states that proportions of nucleotides of the same base pair are approximately equal within single DNA strands. Results of extensive empirical studies using asymmetry measures and various visualization tools show that for long DNA sequences (approximate) strand symmetry generally holds with rather rare exceptions. In the paper, a formal definition of DNA strand local symmetry is presented, characterized in terms of generalized logits and tested for the longest non-coding sequences of bacterial genomes. Validity of a special regression-type probabilistic structure of the data is supposed. This structure is compatible with probability distribution of random nucleotide sequences at a steady state of a context-dependent reversible Markov evolutionary process. The null hypothesis of strand local symmetry is rejected in majority of bacterial genomes suggesting that even neutral mutations are skewed with respect to leading and lagging strands.

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Biographies

Radavičius Marijus

marijus.radavicius@mii.vu.lt

M. Radavičius, Assoc. Prof. Dr., is a senior researcher at Institute of Data Science and Digital Technologies and a professor at Institute of Applied Mathematics, Vilnius University. He received a PhD degree (probability and statistics) in 1982 from the Steklov Institute of Mathematics of Russian Academy of Sciences (St. Petersburg Department). His major research interests include asymptotic statistics, nonparametric and adaptive estimation, dimension reduction and data sparsity, cluster analysis, applications of statistics in life sciences, medicine, linguistics and education.

Rekašius Tomas

tomas.rekasius@vgtu.lt

T. Rekašius, Assoc. Prof. Dr., is working at Department of Mathematical Statistics, Vilnius Gediminas Technical University. He received a PhD degree (mathematics) in 2007 from Vilnius Gediminas Technical University and Institute of Mathematics and Informatics, Vilnius. His major research interests include bioinformatics, applications of statistics in life sciences and medicine.

Židanavičiūtė Jurgita

jurgita.zidanaviciute@vgtu.lt

J. Židanavičiūtė, Dr., received a master’s degree in statistics from 2003 and a PhD degree in mathematics from 2010 from Vilnius Gediminas Technical University. She has been working at Vilnius Gediminas Technical University for 15 years. Her major research interests is applications of statistics in engineering, medicine and other fields.

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Keywords

generalized logit DNA strand symmetry Markov random field characterization hypothesis testing

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