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Authors: E. V. Korotkov 1 ; F. E. Frenkel 1 and M. A. Korotkova 2

Affiliations: 1 Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Russian Federation ; 2 National Research Nuclear University “MEPhI”, Russian Federation

Keyword(s): Sequence, Dynamic Programming, Repeat, Genome, Matrix.

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 A.thaliana genome. 13997 regions having a periodicity with length of 2 to 50 bases were found. The average distance between regions with periodicity is ~9000 nucleotides. A significant portion of the revealed regions have periods consisting of 2 nucleotide, 10-11 nucleotides and periods in the vicinity of 30 nucleotides. No more than ~30% of the periods found were discovered early. The sequences found were collected in a data bank from the website: http://victoria.biengi.ac.ru/cgi-in/indelper/index.cgi. This study discussed the origin of periodicity with i nsertions and deletions. (More)

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Paper citation in several formats:
Korotkov, E.; Frenkel, F. and Korotkova, M. (2017). Search of Periodicity Regions in the Genome A.thaliana. In Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017) - BIOINFORMATICS; ISBN 978-989-758-214-1; ISSN 2184-4305, SciTePress, pages 125-132. DOI: 10.5220/0006106001250132

@conference{bioinformatics17,
author={E. V. Korotkov. and F. E. Frenkel. and M. A. Korotkova.},
title={Search of Periodicity Regions in the Genome A.thaliana},
booktitle={Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017) - BIOINFORMATICS},
year={2017},
pages={125-132},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006106001250132},
isbn={978-989-758-214-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017) - BIOINFORMATICS
TI - Search of Periodicity Regions in the Genome A.thaliana
SN - 978-989-758-214-1
IS - 2184-4305
AU - Korotkov, E.
AU - Frenkel, F.
AU - Korotkova, M.
PY - 2017
SP - 125
EP - 132
DO - 10.5220/0006106001250132
PB - SciTePress

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