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

Author

Listed:
  • 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)

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 .

Suggested Citation

  • 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 &, 2021. "R2DT is a framework for predicting and visualising RNA secondary structure using templates," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23555-5
    DOI: 10.1038/s41467-021-23555-5
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    Cited by:

    1. Patrick C. Hoffmann & Jan Philipp Kreysing & Iskander Khusainov & Maarten W. Tuijtel & Sonja Welsch & Martin Beck, 2022. "Structures of the eukaryotic ribosome and its translational states in situ," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Wenkai Wang & Chenjie Feng & Renmin Han & Ziyi Wang & Lisha Ye & Zongyang Du & Hong Wei & Fa Zhang & Zhenling Peng & Jianyi Yang, 2023. "trRosettaRNA: automated prediction of RNA 3D structure with transformer network," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Luis E. Valentin-Alvarado & Kathryn E. Appler & Valerie Anda & Marie C. Schoelmerich & Jacob West-Roberts & Veronika Kivenson & Alexander Crits-Christoph & Lynn Ly & Rohan Sachdeva & Chris Greening & , 2024. "Asgard archaea modulate potential methanogenesis substrates in wetland soil," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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