Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming

Pugacheva Valentina, Korotkov Alexander and Korotkov Eugene ()
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Pugacheva Valentina: Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
Korotkov Alexander: National Research Nuclear University “MEPhI”, Kashirskoe shosse, 31. Moscow 115409, Russian Federation
Korotkov Eugene: National Research Nuclear University “MEPhI”, Kashirskoe shosse, 31. Moscow 115409, Russian Federation

Statistical Applications in Genetics and Molecular Biology, 2016, vol. 15, issue 5, 381-400

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 a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze 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.

Keywords: deletions; dynamic programming; periodicity; protein sequences (search for similar items in EconPapers)
Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:bpj:sagmbi:v:15:y:2016:i:5:p:381-400:n:2

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DOI: 10.1515/sagmb-2015-0079

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