ISSN 0869-6632 (Print)
ISSN 2542-1905 (Online)

For citation:

Zimnyakov D. А., Alonova M. V., Skripal A. V., Inkin M. G., Zaytsev S. S., Feodorova V. Polarization- and CGR-based binary representations as identifiers of the nucleotide sequences in bioinformatics. Izvestiya VUZ. Applied Nonlinear Dynamics, 2024, vol. 32, iss. 4, pp. 439-459. DOI: 10.18500/0869-6632-003110, EDN: CGGWGX

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Language: 
Russian
Heading: 
Innovations in applied physics
Article type: 
Article
UDC: 
004.93:577.113.5:535-4
DOI: 
10.18500/0869-6632-003110
EDN: 
CGGWGX

Polarization- and CGR-based binary representations as identifiers of the nucleotide sequences in bioinformatics

Autors: 
Zimnyakov Dmitry Александрович, Yuri Gagarin State Technical University of Saratov
Alonova Marina Vasilevna, Yuri Gagarin State Technical University of Saratov
Skripal Anatolij Vladimirovich, Saratov State University
Inkin Maksim Glebovich, Saratov State University
Zaytsev Sergey S,
Feodorova Valentina,
Abstract: 

Purpose of this work is the comparative analysis of two approaches to the synthesis of two-dimensional binary identifiers of nucleotide sequences obtained using DNA sequencing of biological objects.

Methods. One of the approaches is based on modeling the polarization-dependent diffraction of a coherent readout beam on a two-dimensional phase-modulating structure (phase screen) associated with the symbolic sequence obtained as a result of DNA sequencing. Another approach uses a two-dimensional representation of the symbolic sequence using a chaos game representation (CGR). To obtain a finite-element CGR mapping, it is fragmented into a given number of cells, ensuring acceptable sensitivity of the synthesized binary identifier to structural changes in the displayed sequence.

Results. The comparative analysis was carried out using fragments of symbol sequences corresponding to various strains (Wuhan, Delta, Omicron) of the SarSCoV2 virus. In the course of the analysis, the correlation coefficients between the binary identifiers corresponding to various strains were obtained and compared with each other.

Conclusion. It has been established that binary identifiers synthesized using the polarization encoding technique are characterized by significantly higher sensitivity to structural changes in the analyzed sequences and smaller sizes compared to CGR binary identifiers.

Key words: 
nucleotide sequences
binary representation
polarization encoding
chaos game representation
Acknowledgments: 
This work was supported by the Russian Science Foundation, grant No. 22-21-00194
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Received: 
07.11.2023
Accepted: 
28.02.2024
Available online: 
28.05.2024
Published: 
31.07.2024
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