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Authors: Valentina Pugacheva 1 ; Alexander Korotkov 2 and Eugene Korotkov 1

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

Keyword(s): Genetic Algorithm, Latent Periodicity, Dynamic Programming, Amino Acid Sequences.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Sequence Analysis

Abstract: The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming, and random weight matrices were used to develop the new mathematical algorithm for latent periodicity search. The method makes the direct optimization of the position-weight matrix for multiple sequence alignment without using pairwise alignments. The developed algorithm was applied to analyze the amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.

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Paper citation in several formats:
Pugacheva, V.; Korotkov, A. and Korotkov, E. (2016). Search for Latent Periodicity in Amino Acid Sequences with Insertions and Deletions. In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS; ISBN 978-989-758-170-0; ISSN 2184-4305, SciTePress, pages 117-127. DOI: 10.5220/0005630401170127

@conference{bioinformatics16,
author={Valentina Pugacheva. and Alexander Korotkov. and Eugene Korotkov.},
title={Search for Latent Periodicity in Amino Acid Sequences with Insertions and Deletions},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS},
year={2016},
pages={117-127},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005630401170127},
isbn={978-989-758-170-0},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) - BIOINFORMATICS
TI - Search for Latent Periodicity in Amino Acid Sequences with Insertions and Deletions
SN - 978-989-758-170-0
IS - 2184-4305
AU - Pugacheva, V.
AU - Korotkov, A.
AU - Korotkov, E.
PY - 2016
SP - 117
EP - 127
DO - 10.5220/0005630401170127
PB - SciTePress

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