Polarization Analysis of Gene Sequence Structures: Mapping of Extreme Local Polarization States

Dmitry A. Zimnyakov; Marina V. Alonova; Anatoly V. Skripal; Sergey S. Zaitsev; Valentina A. Feodorova

doi:10.18287/JBPE22.08.040302

Authors

Dmitry A. Zimnyakov Yury Gagarin State Technical University of Saratov, Russia Institute for Precision Mechanics and Control Problems of the Russian Academy of Sciences (IPTMU RAS), Saratov, Russia http://orcid.org/0000-0002-9787-7903 (unauthenticated)
Marina V. Alonova Yury Gagarin State Technical University of Saratov, Russia http://orcid.org/0000-0001-7772-3985 (unauthenticated)
Anatoly V. Skripal Saratov State University, Russia http://orcid.org/0000-0002-9080-0057 (unauthenticated)
Sergey S. Zaitsev Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia
Valentina A. Feodorova Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia http://orcid.org/0000-0002-3827-407X (unauthenticated)

DOI:

https://doi.org/10.18287/JBPE22.08.040302

Keywords:

gene sequences, nucleotide triplets, phase screen, diffraction, Stokes vector components, extreme states, binary distributions

Abstract

A method for visualization and identification of nucleotide sequences is proposed based on the synthesis of phase screens displaying the structure of the analyzed sequences and reconstruction of binary maps of the extreme values of the local Stokes vector components in the diffraction zone. This diffraction zone is formed due to reading out the phase screen by a coherent collimated beam with two orthogonally polarized (x–y) components. With different phase delays of the x–y components of the readout beam introduced by the phase screen elements, this causes a variety of local polarization states in the diffraction zone. The discrimination level for the local component of the Stokes vector chosen for the binary mapping is established near the extreme value for this component. Computer verification of the proposed method using nucleotide sequences for various strains of the model African swine fewer (ASF) virus as the test objects shows its high efficiency in the detection of differences between two compared sequences corresponding to the same type of infectious agent. Analysis of the model data for the strains under study made it possible to establish a power-law character of correlation coefficients of the synthesized binary distributions of extreme local polarization states depending on the discrimination threshold detuning from the maximum value of the Stokes vector component used for the mapping.

Author Biographies

Dmitry A. Zimnyakov, Yury Gagarin State Technical University of Saratov, Russia Institute for Precision Mechanics and Control Problems of the Russian Academy of Sciences (IPTMU RAS), Saratov, Russia

Doctor of Sciences in Physics and Mathematics, Professor. Works as Head of Physics Department of the Yury Gagarin State Technical University of Saratov. Research interests: statistical optics, laser physics, photonics.
Marina V. Alonova, Yury Gagarin State Technical University of Saratov, Russia

Candidate of physical and mathematical sciences. Associate professor of Physics Department, deputy director for scientific work of Institute of physics and technology of Yury Gagarin State Technical University of Saratov. Research interests: mathematical modeling, laser physics, statistical optics, photonics.
Anatoly V. Skripal, Saratov State University, Russia

Doctor of Physical and Mathematical Sciences, Professor. He works as the head of the Department of Medical Physics at the Saratov National Research State University named after N.G. Chernyshevsky. Research interests: laser physics, biotechnical systems, photonics, medical physics
Sergey S. Zaitsev, Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia

Works in laboratory of molecular biology and nanobiotechnology Federal Research Center for Virology and Microbiology, researcher. Research interests: molecular microbiology, genes, sequencing, bioinformatics, pathogens of infections in animals and humans
Valentina A. Feodorova, Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia

Doctor of medical sciences, professor. Head of the laboratory of molecular biology and nanobiotechnology, chief researcher. Research interests: molecular microbiology and immunology, digital biology, genes, sequencing, animal and human pathogens.

References

S. Kumar, G. S. Kumar, S. S. Maitra, P. Malý, S. Bharadwaj, P. Sharma, and V. D. Dwivedi, “Viral informatics: bioinformatics-based solution for managing viral infections,” Briefings in Bioinformatics 23(5), bbac326 (2022).

S. Goodwin, J. D. McPherson, and W. R. McCombie, “Coming of age: ten years of next-generation sequencing technologies,” Nature Reviews Genetics 17, 333–351 (2016).

N. N. Pozdnichenko, M. S. Stupin, A. S. Gumenyuk, M. S. Doroshenko, and O. P. Shafeeva, “Algorithms and software for obtaining dissimilar order and high order of symbolic sequences,” Journal of Physics: Conference Series 1050(1), 012063 (2018).

S. S. Ulyanov, O. V. Ulianova, S. S. Zaytsev, Y. V. Saltykov, and V. A. Feodorova, “Statistics on gene-based laser speckles with a small number of scatterers: implications for the detection of polymorphism in the Chlamydia trachomatis omp1 gene,” Laser Physics Letters 15(4), 045601 (2017).

S. S. Ulyanov, S. S. Zaytsev, O. V. Ulianova, Y. V. Saltykov, and V. A. Feodorova, “Using of methods of speckle optics for Chlamydia trachomatis typing,” Proceedings of SPIE 10336, 103360D (2017).

J. W. Goodman, Statistical Optics, 2nd ed., John Wiley & Sons, Hoboken, New Jersey, USA (2015). ISBN: 978-1-119-00945-0.

J. W. Goodman, Introduction to Fourier Optics, 3rd ed., Publishers, Englewood, Colorado, USA (2005). ISBN: 978-0974707723.

A. Mazloum, A. van Schalkwyk, A. Shotin, A. Igolkin, I. Shevchenko, K. Gruzdev, and N. Vlasova, “Comparative Analysis of Full Genome Sequences of African Swine Fever Virus Isolates Taken from Wild Boars in Russia in 2019,” Pathogens 10(5), 521 (2021).

D. Beltran-Alcrudo, M. A. C. C. Gallardo, S. A. Kramer, M. L. Penrith, A. Kamata, and L. Wiersma, African swine fever: detection and diagnosis, Food and Agriculture Organization of the United Nations (FAO), Rome, Italy (2017). ISBN: 978-92-5-109752-6.

R. Bracewell, The Fourier Transform and Its Applications, 2nd ed., McGraw Hill, New York, USA (1986). ISBN 978-0070070165.