Kerpedjiev Peter, Hammer Stefan, Hofacker Ivo L
Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and.
Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währinger Straße 29, A-1090 Vienna, Austria.
Bioinformatics. 2015 Oct 15;31(20):3377-9. doi: 10.1093/bioinformatics/btv372. Epub 2015 Jun 22.
The secondary structure of RNA is integral to the variety of functions it carries out in the cell and its depiction allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant. Current approaches to visualizing secondary structure provide an adequate platform for the conversion of static text-based representations to 2D images, but are limited in their offer of interactivity as well as their ability to display larger structures, multiple structures and pseudoknotted structures.
In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files. It requires no software installation apart from a modern web browser.
The web interface of forna is available at http://rna.tbi.univie.ac.at/forna while the source code is available on github at www.github.com/pkerpedjiev/forna.
Supplementary data are available at Bioinformatics online.
RNA的二级结构对于其在细胞中执行的各种功能至关重要，对其进行描绘有助于研究人员就哪些核苷酸和碱基对具有功能相关性提出假设。当前用于可视化二级结构的方法为将基于文本的静态表示转换为二维图像提供了一个合适的平台，但在交互性以及显示更大结构、多个结构和假结结构的能力方面存在局限性。
在本文中，我们展示了forna，这是一个基于网络的用于显示RNA二级结构的工具，它允许用户轻松地将序列和二级结构转换为清晰、简洁且可定制的可视化形式。它支持多种功能，包括同时可视化多个结构、显示假结结构、对显示的结构进行交互式编辑以及从PDB文件自动生成二级结构图。除了现代网络浏览器外，无需安装任何软件。
forna的网络界面可在http://rna.tbi.univie.ac.at/forna获取，而源代码可在github上的www.github.com/pkerpedjiev/forna获取。
补充数据可在《生物信息学》在线获取。
