RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server for single sequence RNA secondary structure prediction including pseudoknots. pknotsRG employs the newest Turner energy rules for finding the structure of minimal free energy. The algorithm has been improved in several ways recently. First, it has been reimplemented in the C programming language, resulting in a 60-fold increase in speed. Second, all suboptimal foldings up to a user-defined threshold can be enumerated. For large scale analysis, a fast sliding window mode is available. Further improvements of the Web Server are a new output visualization using the PseudoViewer Web Service or RNAmovies for a movie like animation of several suboptimal foldings.The tool is available as source code, binary executable, online tool or as Web Service. The latter alternative allows for an easy integration into bio-informatics pipelines. pknotsRG is available at the Bielefeld Bioinformatics Server ().
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机译：RNA假结是RNA的重要结构特征，但由于效率原因，在计算机预测中经常被忽略。在这里，我们介绍了用于单序列RNA二级结构预测（包括假结）的pknotsRG Web服务器。 pknotsRG使用最新的Turner能量规则来查找最小自由能的结构。最近，该算法已通过多种方式进行了改进。首先，它已用C编程语言重新实现，从而使速度提高了60倍。第二，可以列举所有低于用户定义阈值的次优折叠。对于大规模分析，可以使用快速滑动窗口模式。 Web Server的进一步改进是使用PseudoViewer Web Service或RNAmovies进行的新输出可视化，用于电影等具有次佳折叠效果的动画。该工具可以作为源代码，二进制可执行文件，在线工具或Web Service使用。后一种选择允许轻松集成到生物信息学管道中。可以在Bielefeld Bioinformatics Server（）上找到pknotsRG。
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