Department of Computer Science, Centre for High-Throughput Biology, University of British Columbia, Vancouver V6T 1Z4, Canada.
Nucleic Acids Res. 2012 Jul;40(12):e95. doi: 10.1093/nar/gks241. Epub 2012 Mar 19.
Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems.
直观地检查 RNA 结构可以极大地帮助理解其潜在的功能作用，并评估结构预测算法的性能。由于 RNA 的二级结构已经可以研究许多 RNA 结构的功能作用，因此已经设计了各种用于可视化 RNA 二级结构的方法。这些方法中的大多数将给定的 RNA 二级结构描绘为一个由碱基配对的茎通过圆形环相互连接的平面图形。在本文中，我们提出了一种将 RNA 二级结构描绘为弧图的替代方法。对于难以或不可能表示为平面茎环图的结构，这种方法非常适合。弧图可以直观地显示伪结结构以及瞬态和替代结构特征。此外，它们还方便了已知和预测的 RNA 二级结构的比较。另一个好处是可以结合相应的多重序列比对来显示结构信息，从而突出结构和一级序列的保守性和变异性。我们已经将可视化算法实现为一个名为 R-chie 的网络服务器，以及一个名为 R4RNA 的相应 R 包，该包允许用户在本地以及一系列常见的操作系统上运行该软件。
