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

Loren Dean Williams,Patricia P Chan,David Hoksza,Fábio Madeira,Robert D Finn,Anton S Petrov,Todd M Lowe,Blake A Sweeney,Carlos Eduardo Ribas,Jamie J Cannone,Robin Gutell,Anton I Petrov,Aparna Maddala,Eric P Nawrocki,Caeden D Meade

doi:10.1038/s41467-021-23555-5

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.

Highlights

Non-coding RNAs are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure
Visualisations may (1) Use dot plots where the X and Y axes represent the RNA sequence and the base pairs are shown as dots in Cartesian space; or (2) Arc plots[5] which represent the RNA as a line and interactions as arcs connecting paired nucleotides; and (3) Circular diagrams, which are effectively arc diagrams folded into a circle
To speed up template selection, the library is divided into several subsets which are processed separately (Rfam, LSU and SSU RiboVision ribosomal RNA (rRNA), Comparative RNA Web Site2 (CRW), and transfer RNA (tRNA) templates)

Summary

Introduction

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. TRNAs are traditionally displayed in a cloverleaf layout with the 5′- and 3′- ends located at the top, the anticodon loop pointing towards the bottom, and the D- and T- loops facing left and right, respectively[3]. Both of these representations capture important structural and functional features, providing valuable insights into the RNA structure and function. Visualisations may (1) Use dot plots where the X and Y axes represent the RNA sequence and the base pairs are shown as dots in Cartesian space (for example iDotter4); or (2) Arc plots[5] which represent the RNA as a line and interactions as arcs connecting paired nucleotides (for example R-Chie6); and (3) Circular diagrams, which are effectively arc diagrams folded into a circle (for example VARNA7)

Methods

Results

Conclusion