Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia.
Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia.
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae495.
Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions.
We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool's capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms.
R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.
长读 RNA 测序能够以单个转录本异构体的分辨率绘制 RNA 修饰、结构和蛋白质相互作用位点的图谱。为了理解这些 RNA 特征的功能，关键是要在转录组和基因组注释（如开放阅读框和剪接接头）的背景下对其进行分析。
我们开发了 R2Dtool，这是一种生物信息学工具，它将转录本映射信息与转录本和基因组注释集成在一起，允许对 RNA 特征进行异构体解析分析，并以其基因组背景进行图形表示。我们展示了 R2Dtool 整合和加速 RNA 特征分析的能力，使用了表观转录组学数据。R2Dtool 有助于对替代转录本异构体进行全面分析和解释。
R2Dtool 根据麻省理工学院的许可证免费提供，可在 github.com/comprna/R2Dtool 上获得。
