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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

. 2021 ; 12 (1) : 3494. [pub] 20210609

Jazyk angličtina Země Velká Británie

Typ dokumentu časopisecké články, Research Support, N.I.H., Intramural, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz   https://www.medvik.cz/link/bmc21018461

Grantová podpora
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

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 .

Citace poskytuje Crossref.org

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$a Hoksza, David $u Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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