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Search of Regions with Periodicity Using Random Position Weight Matrices in the Genome of C. elegans

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Bioinformatics and Biomedical Engineering (IWBBIO 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10209))

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Abstract

A mathematical method was developed in this study to determine tandem repeats in a DNA sequence. A multiple alignment of periods was calculated by direct optimization of the position-weight matrix (PWM) without using pairwise alignments or searching for similarity between periods. Random PWMs were used to develop a new mathematical algorithm for periodicity search. The developed algorithm was applied to analyze the DNA sequences of C. elegans genome. 25360 regions having a periodicity with length of 2 to 50 bases were found. On the average, a periodicity of ~4000 nucleotides was found to be associated with each region. A significant portion of the revealed regions have periods consisting of 10 and 11 nucleotides, multiple to 10 nucleotides and periods in the vicinity of 35 nucleotides. Only ~30% of the periods found were discovered early. This study discussed the origin of periodicity with insertions and deletions.

This work was supported by Russian Science Foundation.

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Acknowledgements

This work was supported by Competitiveness Growth Program of the Federal Autonomous Educational Institution of Higher Professional Education National Research Nuclear University MEPhI (Moscow Engineering Physics Institute).

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Authors and Affiliations

  1. Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071, Moscow, Russia

    E. V. Korotkov

  2. National Research Nuclear University “MEPhI”, Kashirskoe shosse, 31, Moscow, 115409, Russia

    E. V. Korotkov & M. A. Korotkova

Authors
  1. E. V. Korotkov
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  2. M. A. Korotkova
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Correspondence to E. V. Korotkov .

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Editors and Affiliations

  1. Universidad de Granada, Granada, Spain

    Ignacio Rojas

  2. Universidad de Granada, Granada, Spain

    Francisco Ortuño

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Korotkov, E.V., Korotkova, M.A. (2017). Search of Regions with Periodicity Using Random Position Weight Matrices in the Genome of C. elegans . In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_40

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  • DOI: https://doi.org/10.1007/978-3-319-56154-7_40

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  • Online ISBN: 978-3-319-56154-7

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