R2DT is a framework for predicting and visualising RNA secondary structure using templates

Blake A. Sweeney, David Hoksza, Eric P. Nawrocki, Carlos Eduardo Ribas, Fábio Madeira, Jamie J. Cannone, Robin Gutell, Aparna Maddala, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Patricia P. Chan, Todd M. Lowe, Robert D. Finn and Anton I. Petrov ()
Additional contact information
Blake A. Sweeney: European Bioinformatics Institute
David Hoksza: Charles University
Eric P. Nawrocki: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Carlos Eduardo Ribas: European Bioinformatics Institute
Fábio Madeira: European Bioinformatics Institute
Jamie J. Cannone: The University of Texas at Austin
Robin Gutell: The University of Texas at Austin
Aparna Maddala: Georgia Institute of Technology
Caeden D. Meade: Georgia Institute of Technology
Loren Dean Williams: Georgia Institute of Technology
Anton S. Petrov: Georgia Institute of Technology
Patricia P. Chan: University of California Santa Cruz
Todd M. Lowe: University of California Santa Cruz
Robert D. Finn: European Bioinformatics Institute
Anton I. Petrov: European Bioinformatics Institute

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
https://www.nature.com/articles/s41467-021-23555-5 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23555-5

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-23555-5

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().