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.

Department of Biomedical Data Science Stanford University Palo Alto CA 94305 5102 United States

Department of Biomolecular Engineering Baskin School of Engineering University of California Santa Cruz CA 95064 United States

Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 United States

Department of Mathematics and Statistics Bowling Green State University Bowling Green OH 43403 United States

Department of Software Engineering Charles University Prague 118 00 Czech Republic

European Molecular Biology Laboratory Wellcome Genome Campus European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom

Faculty of Life Sciences University of Strasbourg Strasbourg 67000 France

Independent Researcher Tbilisi Georgia

NASA Center for Integration of the Origin of Life Georgia Institute of Technology Atlanta GA 30332 0400 United States

National Center for Biotechnology Information U S National Library of Medicine National Institutes of Health Bethesda MD 20894 United States

Riboscope Ltd 23 King Street Cambridge CB1 1AH United Kingdom

School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 0400 United States

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bioRxiv. 2024 Sep 30:2024.09.29.611006. doi: 10.1101/2024.09.29.611006. PubMed

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