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

Blake Sweeney(European Bioinformatics Institute), David Hoksza(Charles University), Eric P. Nawrocki(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 R. 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(European Bioinformatics Institute), Patricia P. Chan(University of California, Santa Cruz), Todd M. Lowe(University of California, Santa Cruz), ROBERT FINN(European Bioinformatics Institute), Anton I. Petrov(European Bioinformatics Institute)
Nature Communications
June 9, 2021
10.1038/s41467-021-23555-5
Cited by 147Open Access
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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 .

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