Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Zimnyakov, Dmitry, Alonova, Marina, Skripal, Anatoly, Dobdin, Sergey, Feodorova, Valentina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
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
_version_ 1784894296448565248
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
work_keys_str_mv AT zimnyakovdmitry quantificationofthediversityingenestructuresusingtheprinciplesofpolarizationmapping
AT alonovamarina quantificationofthediversityingenestructuresusingtheprinciplesofpolarizationmapping
AT skripalanatoly quantificationofthediversityingenestructuresusingtheprinciplesofpolarizationmapping
AT dobdinsergey quantificationofthediversityingenestructuresusingtheprinciplesofpolarizationmapping
AT feodorovavalentina quantificationofthediversityingenestructuresusingtheprinciplesofpolarizationmapping