jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs
jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs
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DOI：
10.1371/journal.pone.0210281
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发表时间：
2019-05-06
期刊：
影响因子：
3.7
通讯作者：
Wiese, Kay C.
中科院分区：
文献类型：
--
作者：
Shabash, Boris;Wiese, Kay C.
在此之前，我们已经介绍了一个改进版本的jViz.RNA，它通过使用压缩树图实现了更快，更稳定的RNA可视化。然而，新的RNA表示和可视化方法需要一个复杂的机制，假结可视化。在这项工作中，我们提出了我们的新的伪结分类和实现的伪结可视化的背景下，新的RNA图模型。然后，我们将我们的方法与其他RNA可视化软件进行比较，并展示了jViz.RNA4.0与其他软件相比的优势。此外，我们将交互式编辑功能引入jViz.RNA，并展示了其在探索和构建RNA结构方面的优势。呈现的结果突出了jViz.RNA 4.0现在提供的新的高度实用性。用户现在能够可视化假结RNA，操纵产生的自动布局以满足他们的个人需求，并改变所检查的RNA分子的定位和连接。注意限制结构元件之间的重叠，特别是在假结的情况下，以确保最终RNA结构的直观和信息丰富的布局。
Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0's benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure.