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Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping
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 nucleo...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9955201/ https://www.ncbi.nlm.nih.gov/pubmed/36826056 http://dx.doi.org/10.3390/cimb45020111 |
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author | Zimnyakov, Dmitry Alonova, Marina Skripal, Anatoly Dobdin, Sergey Feodorova, Valentina |
author_facet | Zimnyakov, Dmitry Alonova, Marina Skripal, Anatoly Dobdin, Sergey Feodorova, Valentina |
author_sort | Zimnyakov, Dmitry |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9955201 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-99552012023-02-25 Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping Zimnyakov, Dmitry Alonova, Marina Skripal, Anatoly Dobdin, Sergey Feodorova, Valentina Curr Issues Mol Biol Article 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. MDPI 2023-02-18 /pmc/articles/PMC9955201/ /pubmed/36826056 http://dx.doi.org/10.3390/cimb45020111 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zimnyakov, Dmitry Alonova, Marina Skripal, Anatoly Dobdin, Sergey Feodorova, Valentina Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title | Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title_full | Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title_fullStr | Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title_full_unstemmed | Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title_short | Quantification of the Diversity in Gene Structures Using the Principles of Polarization Mapping |
title_sort | quantification of the diversity in gene structures using the principles of polarization mapping |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9955201/ https://www.ncbi.nlm.nih.gov/pubmed/36826056 http://dx.doi.org/10.3390/cimb45020111 |
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