R2DT: a comprehensive platform for visualising RNA secondary structure

Holly McCann; Caeden D. Meade; Loren Dean Williams; Anton S. Petrov; Philip Z. Johnson; Anne E. Simon; David Hoksza; Eric P. Nawrocki; Patricia P. Chan; Todd M. Lowe; Carlos Eduardo Ribas; Blake Sweeney; Fábio Madeira; Stephen Anyango; Sri Devan Appasamy; Mandar Deshpande; Mihály Váradi; Sameer S Velankar; Craig L. Zirbel; Aleksei Naiden; Fabrice Jossinet; Anton I. Petrov

doi:10.1093/nar/gkaf032

BioinformaticsNucleic Acids ResearchFeb 8, 2025

Peer-reviewed journal article

R2DT: a comprehensive platform for visualising RNA secondary structure

Holly McCann iD, Caeden D. Meade iD, Loren Dean Williams iD, Anton S. Petrov iD, Philip Z. Johnson iD, Anne E. Simon iD, David Hoksza iD, Eric P. Nawrocki iD, Patricia P. Chan iD, Todd M. Lowe iD, Carlos Eduardo Ribas iD, Blake Sweeney iD, Fábio Madeira iD, Stephen Anyango iD, Sri Devan Appasamy iD, Mandar Deshpande iD, Mihály Váradi iD, Sameer S Velankar iD, Craig L. Zirbel iD, Aleksei Naiden iD, Fabrice Jossinet iD, Anton I. Petrov iD

Abstract

RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms (SNPs) or SHAPE reactivities. It also offers a new template-free mode allowing visualisation of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualisations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualisation, accessible at https://r2dt.bio.

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