RNApuzzler: efficient outerplanar drawing of RNA-secondary structures
RNApuzzler: efficient outerplanar drawing of RNA-secondary structures
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DOI：
10.1093/bioinformatics/bty817
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发表时间：
2019-04-15
期刊：
影响因子：
5.8
通讯作者：
Zeckzer, Dirk
中科院分区：
文献类型：
--
作者：
Wiegreffe, Daniel;Alexander, Daniel;Zeckzer, Dirk
动机：RNA二级结构是研究RNA功能的有用代表，它捕获了RNA折叠的大部分自由能。利用经验确定的能量参数，可以通过递归算法有效地计算核酸的二级结构。有几个支持这项任务的软件包是现成的。由于RNA二级结构是外平面图，因此可以在平面内不相交地绘制它们。当这些图纸符合一系列超出外平面性的附加约束时，从业者的解释就容易了。这些限制就是RNA提取困难的原因。因此，许多RNA绘制算法并不总是生成无交(外平面)的图。结果：为了弥补这一缺陷，本文提出了保证生成无交(外平面)图的RNApubller算法。它基于一种基于核苷酸距离的约束绘制算法(RNATurtle)。我们研究了允许无交点图形的这些约束的松弛。在这些放松的基础上，我们实现了一个完全自动化、简单和健壮的算法，该算法按照先前建立的指导方针生成美学图形。我们使用RFAM数据库对我们的算法进行了测试，发现我们可以高效地计算其中所有RNA的无交点图形。可用性和实现：该软件可以在以下位置自由访问：https://github.com/dwiegreffe/RNApuzzler.
Motivation: RNA secondary structure is a useful representation for studying the function of RNA, which captures most of the free energy of RNA folding. Using empirically determined energy parameters, secondary structures of nucleic acids can be efficiently computed by recursive algorithms. Several software packages supporting this task are readily available. As RNA secondary structures are outerplanar graphs, they can be drawn without intersection in the plane. Interpretation by the practitioner is eased when these drawings conform to a series of additional constraints beyond outerplanarity. These constraints are the reason why RNA drawing is difficult. Many RNA drawing algorithms therefore do not always produce intersection-free (outerplanar) drawings.Results: To remedy this shortcoming we propose here the RNApuzzler algorithm which is guaranteed to produce intersection-free drawings. It is based on a drawing algorithm respecting constraints based on nucleotide distances (RNAturtle). We investigate relaxations of these constraints allowing for intersection-free drawings. Based on these relaxations, we implemented a fully automated, simple, and robust algorithm that produces aesthetic drawings adhering to previously established guidelines. We tested our algorithm using the RFAM database and found that we can compute intersection-free drawings of all RNAs therein efficiently.Availability and implementation: The software can be accessed freely at: https://github.com/dwiegreffe/RNApuzzler.