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DrawTetrado to create layer diagrams of G4 structures

MOTIVATION: Quadruplexes are specific 3D structures found in nucleic acids. Due to the exceptional properties of these motifs, their exploration with the general-purpose bioinformatics methods can be problematic or insufficient. The same applies to visualizing their structure. A hand-drawn layer dia...

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Detalles Bibliográficos
Autores principales: Zurkowski, Michal, Zok, Tomasz, Szachniuk, Marta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9344840/
https://www.ncbi.nlm.nih.gov/pubmed/35703937
http://dx.doi.org/10.1093/bioinformatics/btac394
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author Zurkowski, Michal
Zok, Tomasz
Szachniuk, Marta
author_facet Zurkowski, Michal
Zok, Tomasz
Szachniuk, Marta
author_sort Zurkowski, Michal
collection PubMed
description MOTIVATION: Quadruplexes are specific 3D structures found in nucleic acids. Due to the exceptional properties of these motifs, their exploration with the general-purpose bioinformatics methods can be problematic or insufficient. The same applies to visualizing their structure. A hand-drawn layer diagram is the most common way to represent the quadruplex anatomy. No molecular visualization software generates such a structural model based on atomic coordinates. RESULTS: DrawTetrado is an open-source Python program for automated visualization targeting the structures of quadruplexes and G4-helices. It generates static layer diagrams that represent structural data in a pseudo-3D perspective. The possibility to set color schemes, nucleotide labels, inter-element distances or angle of view allows for easy customization of the output drawing. AVAILABILITY AND IMPLEMENTATION: The program is available under the MIT license at https://github.com/RNApolis/drawtetrado.
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spelling pubmed-93448402022-08-03 DrawTetrado to create layer diagrams of G4 structures Zurkowski, Michal Zok, Tomasz Szachniuk, Marta Bioinformatics Applications Notes MOTIVATION: Quadruplexes are specific 3D structures found in nucleic acids. Due to the exceptional properties of these motifs, their exploration with the general-purpose bioinformatics methods can be problematic or insufficient. The same applies to visualizing their structure. A hand-drawn layer diagram is the most common way to represent the quadruplex anatomy. No molecular visualization software generates such a structural model based on atomic coordinates. RESULTS: DrawTetrado is an open-source Python program for automated visualization targeting the structures of quadruplexes and G4-helices. It generates static layer diagrams that represent structural data in a pseudo-3D perspective. The possibility to set color schemes, nucleotide labels, inter-element distances or angle of view allows for easy customization of the output drawing. AVAILABILITY AND IMPLEMENTATION: The program is available under the MIT license at https://github.com/RNApolis/drawtetrado. Oxford University Press 2022-06-15 /pmc/articles/PMC9344840/ /pubmed/35703937 http://dx.doi.org/10.1093/bioinformatics/btac394 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Zurkowski, Michal
Zok, Tomasz
Szachniuk, Marta
DrawTetrado to create layer diagrams of G4 structures
title DrawTetrado to create layer diagrams of G4 structures
title_full DrawTetrado to create layer diagrams of G4 structures
title_fullStr DrawTetrado to create layer diagrams of G4 structures
title_full_unstemmed DrawTetrado to create layer diagrams of G4 structures
title_short DrawTetrado to create layer diagrams of G4 structures
title_sort drawtetrado to create layer diagrams of g4 structures
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9344840/
https://www.ncbi.nlm.nih.gov/pubmed/35703937
http://dx.doi.org/10.1093/bioinformatics/btac394
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