Han K, Kim D, Kim H J
Department of Automation Engineering, Inha University, Inchon 402-751 and College of Pharmacy, Chung Ang University, Seoul 156-756, South Korea.
Bioinformatics. 1999 Apr;15(4):286-97. doi: 10.1093/bioinformatics/15.4.286.
To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention.
A new algorithm for automatically drawing RNA secondary structure has been developed. The algorithm represents the direction and space for a structural element using vector and vector space. Two heuristics are used. The first heuristic is concerned with ordering structural elements to be positioned and the second with positioning them in space. The algorithm and a graphical user interface have been implemented in a working program called VizQFolder on IBM PC compatibles. Experimental results demonstrate that VizQFolder is capable of automatically generating nearly overlap-free polygonal displays for long RNA molecules. The only distortion performed to avoid overlap is the rotation of helices, leading to efficient generation of a polygonal display without sacrificing its readability. VizQFolder is not coupled to a specific prediction program of RNA secondary structure, and thus can be used for visualizing secondary structure models obtained by any means.
The executable code of VizQFolder is available at http://automation.inha.ac.kr/khan. It can also be obtained from the authors upon request.
生成RNA二级结构的多边形展示，使结构元件的重叠和扭曲最小化，定位它们时的搜索过程最少，且用户干预最少。
开发了一种自动绘制RNA二级结构的新算法。该算法使用向量和向量空间来表示结构元件的方向和空间。使用了两种启发式方法。第一种启发式方法涉及对要定位的结构元件进行排序，第二种则是在空间中对它们进行定位。该算法和图形用户界面已在一个名为VizQFolder的工作程序中实现，该程序可在IBM PC兼容机上运行。实验结果表明，VizQFolder能够为长RNA分子自动生成几乎无重叠的多边形展示。为避免重叠而进行的唯一扭曲是螺旋的旋转，从而在不牺牲可读性的情况下高效生成多边形展示。VizQFolder不与特定的RNA二级结构预测程序耦合，因此可用于可视化通过任何方式获得的二级结构模型。
VizQFolder的可执行代码可在http://automation.inha.ac.kr/khan获取。也可应作者要求从作者处获得。
