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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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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. |
format | Online Article Text |
id | pubmed-9344840 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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