R2DT：一个用于可视化RNA二级结构的综合平台。

R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.

作者信息

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

机构信息

NASA Center for Integration of the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.

出版信息

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

DOI:10.1101/2024.09.29.611006

PMID:39803519

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11722224/

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.

摘要

RNA二级（二维）结构可视化是理解RNA功能的重要工具。R2DT是一个软件包，旨在以一致、可识别和可重复的布局可视化RNA二维结构。最新版本R2DT 2.0引入了多个重要功能，包括显示位置特异性信息的能力，如单核苷酸多态性（SNP）或SHAPE反应性。它还提供了一种新的无模板模式，允许在没有预先存在模板的情况下可视化RNA，同时还有一种受限折叠模式并支持动画可视化。用户可以手动或使用自然语言提示交互式修改R2DT图，以生成新模板或创建具有发表质量的图像。此外，R2DT具有更快的性能、扩展的模板库以及越来越多的兼容工具和实用程序。R2DT已集成到多个生物数据库中，已发展成为一个用于RNA二维可视化的综合平台，可通过https://r2dt.bio访问。