Han Kyungsook, Byun Yanga
School of Computer Science and Engineering, Inha University, Inchon 402-751, Korea.
Nucleic Acids Res. 2003 Jul 1;31(13):3432-40. doi: 10.1093/nar/gkg539.
Visualizing RNA pseudoknot structures is computationally more difficult than depicting RNA secondary structures, because a drawing of a pseudoknot structure is a graph (and possibly a nonplanar graph) with inner cycles within the pseudoknot, and possibly outer cycles formed between the pseudoknot and other structural elements. We previously developed PSEUDOVIEWER for visualizing H-type pseudoknots. PSEUDOVIEWER2 improves on the first version in many ways: (i) PSEUDOVIEWER2 is more general because it can visualize a pseudoknot of any type, including H-type pseudoknots, as a planar graph; (ii) PSEUDOVIEWER2 computes a drawing of RNA structures much more efficiently and is an order of magnitude faster in actual running time; and (iii) PSEUDOVIEWER2 is a web-based application program. Experimental results demonstrate that PSEUDOVIEWER2 generates an aesthetically pleasing drawing of pseudoknots of any type and that the new representation offered by PSEUDOVIEWER2 ensures uniform and clear drawings, with no edge crossing, for all types of pseudoknots. The PSEUDOVIEWER2 algorithm is the first developed for the automatic drawing of RNA secondary structures, including pseudoknots of any type. PSEUDOVIEWER2 is accessible at http://wilab.inha.ac.kr/pseudoviewer2/.
可视化RNA假结结构在计算上比描绘RNA二级结构更困难，因为假结结构的图形是一个带有假结内部循环的图（可能是非平面图），并且可能在假结与其他结构元件之间形成外部循环。我们之前开发了PSEUDOVIEWER来可视化H型假结。PSEUDOVIEWER2在许多方面对第一个版本进行了改进：（i）PSEUDOVIEWER2更通用，因为它可以将任何类型的假结（包括H型假结）可视化为平面图；（ii）PSEUDOVIEWER2计算RNA结构图形的效率更高，实际运行时间快一个数量级；（iii）PSEUDOVIEWER2是一个基于网络的应用程序。实验结果表明PSEUDOVIEWER2能生成任何类型假结的美观图形，并且PSEUDOVIEWER2提供的新表示确保了所有类型假结的图形均匀且清晰，没有边交叉。PSEUDOVIEWER2算法是首个开发用于自动绘制包括任何类型假结的RNA二级结构的算法。可通过http://wilab.inha.ac.kr/pseudoviewer2/访问PSEUDOVIEWER2。
