Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms

Author:

Chaley M.B.,Kutyrkin V.A.,Tyulbasheva G.E.,Teplukhina E.I.,Nazipova N.N.

Abstract

Analysis of the data from the first release of HeteroGenome database, collecting the revealed regions of latent periodicity in the genomes of a number of eukaryotic organisms, is presented. Tandem repeats with different conservation of a pattern copies, including the highly diverged repeats, were identified in the genomes of S. cerevisiae, A. thaliana, C. elegans and D. melanogaster. The data were obtained with the help of original spectral-statistical approach to searching for the reliable regions of latent periodicity in DNA sequences. Introduction of the two-level structure for the data presentation (At the first, nonredundant level the regions of latent periodicity is generally viewed, at the second level only the fragments of conservative periodic structure are considered.) allowed to estimate a share of genome coverage by the regions of latent periodicity which counts ~10% of a whole genome length. The estimate is deduced according to the data of the first level. An analysis of quantitative and qualitative content (corresponding to the divergence levels) of the latent periodicity regions over all the chromosomes of the considered organisms revealed the characteristic types of periodicity in a genome of each organism. The histograms showing density distribution of the latent periodicity regions along every chromosome in the analyzed genomes were built. A repertoire of period lengths were revealed in the genomes. Moreover, HeteroGenome base offers some additional possibilities for its’ data analysis and is freely available at URL: http://www.jcbi.ru/lp_baze/.

Publisher

Institute of Mathematical Problems of Biology of RAS (IMPB RAS)

Subject

Applied Mathematics,Biomedical Engineering

Cited by 5 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. The IMPB RAS is 50 years old. Bioinformatics Laboratory;Proceedings of the International Conference "Mathematical Biology and Bioinformatics";2022-10-27

2. The complexity of DNA sequences. Different approaches and definitions;Mathematical Biology and Bioinformatics;2020-11-30

3. Detection in the Genomes of Higher Organisms of Highly Fuzzy Megasatellite Repeats;Proceedings of the International Conference "Mathematical Biology and Bioinformatics";2020-11-01

4. Spectral–Statistical Approach for Revealing Latent Regular Structures in DNA Sequence;Methods in Molecular Biology;2016

5. HeteroGenome: database of genome periodicity;Database;2014-05-24

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