Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, United States.
Department of Chemistry, Yale University, New Haven, CT 06511, United States.
Bioinformatics. 2023 Mar 1;39(3). doi: 10.1093/bioinformatics/btad111.
The increasing availability of RNA structural information that spans many kilobases of transcript sequence imposes a need for tools that can rapidly screen, identify, and prioritize structural modules of interest.
We describe RNA Structural Content Scanner (RSCanner), an automated tool that scans RNA transcripts for regions that contain high levels of secondary structure and then classifies each region for its relative propensity to adopt stable or dynamic structures. RSCanner then generates an intuitive heatmap enabling users to rapidly pinpoint regions likely to contain a high or low density of discrete RNA structures, thereby informing downstream functional or structural investigation.
RSCanner is freely available as both R script and R Markdown files, along with full documentation and test data (https://github.com/pylelab/RSCanner).
越来越多的 RNA 结构信息跨越了数千个转录序列碱基对，这就需要能够快速筛选、识别和优先考虑感兴趣的结构模块的工具。
我们描述了 RNA 结构内容扫描器（RSCanner），这是一种自动化工具，可扫描 RNA 转录本中具有高水平二级结构的区域，然后对每个区域进行分类，以确定其形成稳定或动态结构的相对倾向。然后，RSCanner 生成直观的热图，使用户能够快速确定可能包含高密度或低密度离散 RNA 结构的区域，从而为下游功能或结构研究提供信息。
RSCanner 以 R 脚本和 R Markdown 文件的形式免费提供，同时提供完整的文档和测试数据（https://github.com/pylelab/RSCanner）。
