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4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland

The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2),...

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Autores principales: Bielińska-Wąż, Dorota, Wąż, Piotr, Lass, Anna, Karamon, Jacek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9227292/
https://www.ncbi.nlm.nih.gov/pubmed/35743908
http://dx.doi.org/10.3390/life12060877
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author Bielińska-Wąż, Dorota
Wąż, Piotr
Lass, Anna
Karamon, Jacek
author_facet Bielińska-Wąż, Dorota
Wąż, Piotr
Lass, Anna
Karamon, Jacek
author_sort Bielińska-Wąż, Dorota
collection PubMed
description The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2), cytochrome b (cob), and cytochrome c oxidase subunit 1 (cox1), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics (sequence descriptors) applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin.
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spelling pubmed-92272922022-06-25 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland Bielińska-Wąż, Dorota Wąż, Piotr Lass, Anna Karamon, Jacek Life (Basel) Article The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2), cytochrome b (cob), and cytochrome c oxidase subunit 1 (cox1), are analyzed. The sequences are represented by sets of material points in a 4D space, i.e., 4D-dynamic graphs. As a visualization of the sequences, projections of the graphs into 3D space are shown. The differences between 3D graphs corresponding to European, Asian, and American haplotypes are small. Numerical characteristics (sequence descriptors) applied in the studies can recognize the differences. The concept of creating descriptors of 4D-dynamic graphs has been borrowed from classical dynamics; these are coordinates of the centers or mass and moments of inertia of 4D-dynamic graphs. Based on these descriptors, classification maps are constructed. The concentrations of points in the maps indicate one Polish haplotype (EmPL9) of Asian origin. MDPI 2022-06-10 /pmc/articles/PMC9227292/ /pubmed/35743908 http://dx.doi.org/10.3390/life12060877 Text en © 2022 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
Bielińska-Wąż, Dorota
Wąż, Piotr
Lass, Anna
Karamon, Jacek
4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title_full 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title_fullStr 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title_full_unstemmed 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title_short 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity of Echinococcus multilocularis in Red Foxes in Poland
title_sort 4d-dynamic representation of dna/rna sequences: studies on genetic diversity of echinococcus multilocularis in red foxes in poland
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9227292/
https://www.ncbi.nlm.nih.gov/pubmed/35743908
http://dx.doi.org/10.3390/life12060877
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