R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types

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

Non-coding RNAs (ncRNA) are essential for all life, and the functions of many ncRNAs depend on their secondary (2D) and tertiary (3D) structure. Despite proliferation of 2D visualisation software, there is a lack of methods for automatically generating 2D representations in consistent, reproducible, and recognisable layouts, making them difficult to construct, compare and analyse. Here we present R2DT, a comprehensive method for visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,632 templates representing the majority of known structured RNAs, from small RNAs to the large subunit ribosomal RNA. 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 freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt.