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Matematicheskaya Biologiya i Bioinformatika, 2013, Volume 8, Issue 2, Pages 480–501 (Mi mbb156)  

This article is cited in 4 scientific papers (total in 4 papers)

Bioinformatics

Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms

M. B. Chaleya, V. A. Kutyrkinb, E. I. Teplukhinaa, G. E. Tyulbashevaa, N. N. Nazipovaa

a Institute of mathematical problems of biology, Russian academy of sciences, Pushchino, Moscow Region, 142290, Russia
b Moscow State Technical University n.a. N. E. Bauman, Moscow, 107005, Russia
References:
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 $\sim10\%$ 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/.
Key words: latent periodicity, approximate tandem repeats, genome analysis.
Received 23.07.2013, Published 24.09.2013
Document Type: Article
UDC: 577.322
Language: Russian
Citation: M. B. Chaley, V. A. Kutyrkin, E. I. Teplukhina, G. E. Tyulbasheva, N. N. Nazipova, “Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms”, Mat. Biolog. Bioinform., 8:2 (2013), 480–501
Citation in format AMSBIB
\Bibitem{ChaKutTep13}
\by M.~B.~Chaley, V.~A.~Kutyrkin, E.~I.~Teplukhina, G.~E.~Tyulbasheva, N.~N.~Nazipova
\paper Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms
\jour Mat. Biolog. Bioinform.
\yr 2013
\vol 8
\issue 2
\pages 480--501
\mathnet{http://mi.mathnet.ru/mbb156}
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  • https://www.mathnet.ru/eng/mbb/v8/i2/p480
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    This publication is cited in the following 4 articles:
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
     
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