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

Zimnyakov, Dmitry A.; Алонова, М. В.; Skripal, A. V.; Zaitsev, Sergey S.; Feodorova, Valentina A.

doi:10.18287/jbpe22.08.040302

Cited by 3 publications

(3 citation statements)

References 6 publications

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“…Основная идея данной модификации заключается в разделении CGR отображения на равновеликие ячейки, подсчете числа отображающих точек в пределах каждой ячейки и характеризации ячеек по относительным частотам попадания в них точек. Соответственно, относительная частота как информативный параметр может отображаться в градациях серого цвета [17].…”

Section: Introductionunclassified

“…Очевидно, что изменения в структуре отображаемой символьной последовательности по отношению к референтной последовательности, обусловленные мутационными замещениями В работах [17][18][19] был предложен альтернативный подход к синтезу двумерных бинарных отображений нуклеотидных последовательностей на основе моделирования эффекта поляризационной модуляции когерентного светового пучка ДНК-ассоциированным двумерным фазовым экраном. Подобная модуляция приводит к формированию в дальней зоне дифракции распределения локальных состояний поляризации дифрагировавшего пучка, описываемых тремя компонентами нормированного вектора Стокса.…”

Section: Introductionunclassified

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

Zimnyakov,

Alonova,

Skripal

et al. 2024

AND

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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.

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Section: Introductionunclassified

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

Zimnyakov,

Alonova,

Skripal

et al. 2024

AND

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show abstract

“…As a specific approach to the two-dimensional representation of nucleotide sequences of a finite length, the polarization imaging technique [18,19] should also be noted. This technique is based on modeling the reading of a DNA-associated two-dimensional phase object (quasi-random phase screen) using a coherent light beam with a given polarization state and the subsequent analysis of the local polarization structure of the readout beam in the far diffraction zone.…”

Section: Introductionmentioning

confidence: 99%

Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains

Zimnyakov,

Alonova,

Lavrukhin

et al. 2023

CIMB

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Two approaches to the synthesis of 2D binary identifiers (“fingerprints”) of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).

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Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping

Zimnyakov

Алонова

Skripal

et al. 2023

CIMB

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Results of computational analysis and visualization of differences in gene structures using polarization coding are presented. A two-dimensional phase screen, where each element of which corresponds to a specific basic nucleotide (adenine, cytosine, guanine, or thymine), displays the analyzed nucleotide sequence. Readout of the screen with a coherent beam characterized by a given polarization state forms a diffracted light field with a local polarization structure that is unique for the analyzed nucleotide sequence. This unique structure is described by spatial distributions of local values of the Stokes vector components. Analysis of these distributions allows the comparison of nucleotide sequences for different strains of pathogenic microorganisms and frequency analysis of the sequences. The possibilities of this polarization-based technique are illustrated by the model data obtained from a comparative analysis of the spike protein gene sequences for three different model variants (Wuhan, Delta, and Omicron) of the SARS-CoV-2 virus. Various modifications of polarization encoding and analysis of gene structures and a possibility for instrumental implementation of the proposed method are discussed.

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

Cited by 3 publications

References 6 publications

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

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

Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains

Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping

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