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

Dmitry A. Zimnyakov orcid (Login required)
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

Marina V. Alonova orcid
Yury Gagarin State Technical University of Saratov, Russia

Anatoly V. Skripal orcid
Saratov State University, Russia

Sergey S. Zaitsev
Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia

Valentina A. Feodorova orcid
Federal Research Center for Virology and Microbiology (Saratov Branch), Saratov, Russia


Paper #3526 received 12 Sep 2022; revised manuscript received 24 Oct 2022; accepted for publication 28 Oct 2022; published online 3 Dec 2022.

DOI: 10.18287/JBPE22.08.040302

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.

Keywords

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

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References


1. 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).

2. 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).

3. 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).

4. 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).

5. 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).

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

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

8. 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).

9. 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.

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




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