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R2DT: a comprehensive platform for visualizing RNA secondary structure

H. McCann, CD. Meade, LD. Williams, AS. Petrov, PZ. Johnson, AE. Simon, D. Hoksza, EP. Nawrocki, PP. Chan, TM. Lowe, CE. Ribas, BA. Sweeney, F. Madeira, S. Anyango, SD. Appasamy, M. Deshpande, M. Varadi, S. Velankar, CL. Zirbel, A. Naiden, F....

. 2025 ; 53 (4) : . [pub] 20250208

Language English Country England, Great Britain

Document type Journal Article

Persistent link   https://www.medvik.cz/link/bmc25009913

Grant support
R01 GM085328 NIGMS NIH HHS - United States
20 894 U.S. National Library of Medicine
EMBL
R01HG006753 NIH HHS - United States
308291-00001 United States Department of Agriculture
DGE-1840340 National Science Foundation Graduate Research Fellowship Award
2022065 NSF CEP Register
312990-00001 National Science Foundation
218302/Z/19/Z WT
e-INFRA CZ project
Ministry of Education
NLM NIH HHS - United States
80NSSC24K0344 NASA - United States

RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, 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 or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. 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 visualization, accessible at https://r2dt.bio.

References provided by Crossref.org

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