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R2DT is a framework for predicting and visualising RNA secondary structure using templates
BA. Sweeney, D. Hoksza, EP. Nawrocki, CE. Ribas, F. Madeira, JJ. Cannone, R. Gutell, A. Maddala, CD. Meade, LD. Williams, AS. Petrov, PP. Chan, TM. Lowe, RD. Finn, AI. Petrov
Language English Country Great Britain
Document type Journal Article, Research Support, N.I.H., Intramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.
Grant support
Wellcome Trust - United Kingdom
80NSSC18K1139
Intramural NASA - United States
218302/Z/19/Z
Wellcome Trust - United Kingdom
BB/N019199/1
Biotechnology and Biological Sciences Research Council - United Kingdom
NLK
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- MeSH
- Databases, Nucleic Acid MeSH
- Nucleic Acid Conformation MeSH
- RNA, Untranslated chemistry MeSH
- Reproducibility of Results MeSH
- RNA chemistry MeSH
- Sequence Analysis, RNA MeSH
- Software MeSH
- Computational Biology methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Intramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
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 .
Department of Biomolecular Engineering University of California Santa Cruz Santa Cruz CA USA
Department of Integrative Biology The University of Texas at Austin Austin TX USA
European Molecular Biology Laboratory European Bioinformatics Institute Cambridge UK
References provided by Crossref.org
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