PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
复制标题
DOI：
10.1093/bioinformatics/btp252
复制
发表时间：
2009-06-01
期刊：
影响因子：
5.8
通讯作者：
Han, Kyungsook
中科院分区：
文献类型：
--
作者：
Byun, Yanga;Han, Kyungsook
动机：RNA结构中的伪结使得RNA结构的可视化变得困难。即使一个假结本身没有交叉，整个RNA结构的可视化与假结往往会导致一个假结和其他结构元素之间的交叉绘图，并需要额外的干预，由用户来确保结构图是无交叉的。许多程序（如Web服务）更喜欢一次性获得无重叠图，而不是获得要编辑的重叠图。RNA伪结的可视化程序很少，而PseudoViewer几乎是唯一一个自动绘制RNA二级结构的程序。先前版本的PseudoViewer可视化所有已知类型的RNA pseudoknots作为平面图，但可视化一些假设的pseudoknots作为非平面drawings.Results：我们开发了一个新版本的PseudoViewer，用于有效地可视化大型RNA结构与任何类型的pseudoknots，无论是已知的还是假设的，作为平面图在一个镜头。它比以前的算法快10倍左右，并产生更紧凑和美观的结构图。PseudoViewer3支持Web服务和Web应用程序。
Motivation: Pseudoknots in RNA structures make visualization of RNA structures difficult. Even if a pseudoknot itself is represented without a crossing, visualization of the entire RNA structure with a pseudoknot often results in a drawing with crossings between the pseudoknot and other structural elements, and requires additional intervention by the user to ensure that the structure graph is overlap-free. Many programs such as web services prefer to obtain an overlap-free graph in one-shot rather than get a graph with overlaps to be edited. There are few programs for visualizing RNA pseudoknots, and PseudoViewer has been the almost only program that automatically draws RNA secondary structures with pseudoknots. The previous version of PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some hypothetical pseudoknots as non-planar drawings.Results: We developed a new version of PseudoViewer for efficiently visualizing large RNA structures with any types of pseudoknots, both known and hypothetical, as planar drawings in one-shot. It is about 10 times faster than the previous algorithm, and produces a more compact and aesthetic structure drawing. PseudoViewer3 supports both web services and web applications.