RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs

MOTIVATION: In the study of 3D RNA structure, information about non-canonical interactions between nucleobases is increasingly important. Specialized databases support investigation of this issue based on experimental data, and several programs can annotate non-canonical base pairs in the RNA 3D str...

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Autores principales: Antczak, Maciej, Zablocki, Marcin, Zok, Tomasz, Rybarczyk, Agnieszka, Blazewicz, Jacek, Szachniuk, Marta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298044/
https://www.ncbi.nlm.nih.gov/pubmed/29985979
http://dx.doi.org/10.1093/bioinformatics/bty609
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author Antczak, Maciej
Zablocki, Marcin
Zok, Tomasz
Rybarczyk, Agnieszka
Blazewicz, Jacek
Szachniuk, Marta
author_facet Antczak, Maciej
Zablocki, Marcin
Zok, Tomasz
Rybarczyk, Agnieszka
Blazewicz, Jacek
Szachniuk, Marta
author_sort Antczak, Maciej
collection PubMed
description MOTIVATION: In the study of 3D RNA structure, information about non-canonical interactions between nucleobases is increasingly important. Specialized databases support investigation of this issue based on experimental data, and several programs can annotate non-canonical base pairs in the RNA 3D structure. However, predicting the extended RNA secondary structure which describes both canonical and non-canonical interactions remains difficult. RESULTS: Here, we present RNAvista that allows predicting an extended RNA secondary structure from sequence or from the list enumerating canonical base pairs only. RNAvista is implemented as a publicly available webserver with user-friendly interface. It runs on all major web browsers. AVAILABILITY AND IMPLEMENTATION: http://rnavista.cs.put.poznan.pl
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spelling pubmed-62980442018-12-21 RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs Antczak, Maciej Zablocki, Marcin Zok, Tomasz Rybarczyk, Agnieszka Blazewicz, Jacek Szachniuk, Marta Bioinformatics Applications Notes MOTIVATION: In the study of 3D RNA structure, information about non-canonical interactions between nucleobases is increasingly important. Specialized databases support investigation of this issue based on experimental data, and several programs can annotate non-canonical base pairs in the RNA 3D structure. However, predicting the extended RNA secondary structure which describes both canonical and non-canonical interactions remains difficult. RESULTS: Here, we present RNAvista that allows predicting an extended RNA secondary structure from sequence or from the list enumerating canonical base pairs only. RNAvista is implemented as a publicly available webserver with user-friendly interface. It runs on all major web browsers. AVAILABILITY AND IMPLEMENTATION: http://rnavista.cs.put.poznan.pl Oxford University Press 2019-01-01 2018-07-09 /pmc/articles/PMC6298044/ /pubmed/29985979 http://dx.doi.org/10.1093/bioinformatics/bty609 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://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
Antczak, Maciej
Zablocki, Marcin
Zok, Tomasz
Rybarczyk, Agnieszka
Blazewicz, Jacek
Szachniuk, Marta
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title_full RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title_fullStr RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title_full_unstemmed RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title_short RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
title_sort rnavista: a webserver to assess rna secondary structures with non-canonical base pairs
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298044/
https://www.ncbi.nlm.nih.gov/pubmed/29985979
http://dx.doi.org/10.1093/bioinformatics/bty609
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