Kostenko D. O. (Postgraduate, junior researcher
National Research Nuclear University MEPhI
(Moscow Engineering Physics Institute),
The Federal Research Centre “Fundamentals of Biotechnology”
of the Russian Academy of Sciences (Moscow)
)
Korotkov E. V. (PhD, professor
National Research Nuclear University MEPhI
(Moscow Engineering Physics Institute),
The Federal Research Centre “Fundamentals of Biotechnology”
of the Russian Academy of Sciences (Moscow)
)
Korotkova M. A. (PhD, docent
National Research Nuclear University MEPhI
(Moscow Engineering Physics Institute)
)
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One of the most important tasks in bioinformatics is multiple sequence alignment of nucleotide and amino acid sequences. Previously, we proposed a new mathematical method for the alignment of highly divergent sequences (MAHDS). In this study, the method was adapted to align amino acid sequences using information about correlations of neighboring symbols. Using model amino acid sequences, we have investigated some properties of the method that may allow one to choose the most appropriate parameters for its practical application. The data which make it possible to evaluate the effectiveness and convergence of an optimization procedure that maximizes the sequences similarity function in alignment is presented. The properties of distributions of alignment quality indicators at different stages of MAHDS are described.
Keywords:multiple sequence alignment, dynamic programming, objective function optimization, distribution.
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Citation link:
Kostenko D. O., Korotkov E. V., Korotkova M. A. PROPERTIES OF THE MAHDS METHOD CONSIDERING CHARACTER CORRELATIONS IN THE CONTEXT OF AMINO ACID SEQUENCES ALIGNMENT // Современная наука: актуальные проблемы теории и практики. Серия: Естественные и Технические Науки. -2025. -№05/2. -С. 79-86 DOI 10.37882/2223-2966.2025.05-2.14 |
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