Shabash Boris, Wiese Kay C
School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada.
BMC Bioinformatics. 2017 May 30;18(1):282. doi: 10.1186/s12859-017-1682-0.
RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures. One such tool is jViz.RNA. Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation.
Comparing the compressed graph and detailed graph implementations, we find that the compressed graph produces results more consistent with RNA drawing conventions. However, we also find that employing the compressed graph method requires a more sophisticated initial layout to produce visualizations that would require minimal user interference. Comparing the two numerical integration methods demonstrates the higher stability of the Backward Euler method, and its resulting ability to handle much larger time steps, a high priority feature for any software which entails user interaction.
The work in this manuscript presents the preferred use of compressed graphs to detailed ones, as well as the advantages of employing the Backward Euler method over the Forward Euler method. These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. The results presented demonstrate that both the compressed graph representation, as well as the Backward Euler integrator, greatly enhance the run-time performance and usability. The newest iteration of jViz.RNA is available at https://jviz.cs.sfu.ca/download/download.html .
传统的RNA可视化软件工具呈现的是RNA分子的静态可视化，用户在图像生成后与结果图像进行交互的能力有限。只有少数工具支持动态结构。其中一个工具是jViz.RNA。目前，jViz.RNA采用一种独特的方法来创建RNA分子布局，即将RNA核苷酸映射到一个图中的顶点，我们称之为详细图，然后利用受牛顿力学启发的力系统来计算RNA分子的布局。本文介绍的工作重点是对jViz.RNA进行改进，使其能够根据常见的绘图规范绘制RNA二级结构，并显著提高运行时性能。首先通过提出一种将RNA分子映射到图中的替代方法，我们称之为压缩图，然后对压缩图表示采用先进的数值积分方法来实现这一目标。
比较压缩图和详细图的实现，我们发现压缩图产生的结果更符合RNA绘图规范。然而，我们也发现采用压缩图方法需要更复杂的初始布局才能生成所需用户干预最少的可视化效果。比较两种数值积分方法表明，后向欧拉方法具有更高的稳定性，并且能够处理更大的时间步长，这对于任何需要用户交互的软件来说都是一个高优先级的特性。
本文的工作展示了压缩图相对于详细图的首选使用，以及采用后向欧拉方法优于前向欧拉方法的优势。这些改进产生了更稳定且视觉上更美观的RNA二级结构表示。所展示的结果表明，压缩图表示以及后向欧拉积分器都极大地提高了运行时性能和可用性。jViz.RNA的最新版本可在https://jviz.cs.sfu.ca/download/download.html获取。
