Yang Tzu-Hsien, Lin Yu-Cian, Hsia Min, Liao Zhan-Yi
Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan.
Comput Struct Biotechnol J. 2022 May 18;20:2473-2483. doi: 10.1016/j.csbj.2022.05.028. eCollection 2022.
RNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures. Experimental structure identification approa ches can show the structures of RNA molecules. However, they usually have limits in the resolution and are costly. structure prediction tools are thus primarily relied on for pre-experiment analysis. Various structure prediction models have been developed over the decades. Since these tools are usually used before knowing the actual RNA structures, evaluating and ranking the pile of secondary structure predictions of a given sequence is essential in computational analysis. In this research, we implemented a web service called SSRTool (RNA Secondary Structure prediction Ranking Tool) to assist in the ranking and evaluation of the generated predicted structures of a given sequence. Based on the computed species-specific interpretability significance in four common RNA structure-function aspects, SSRTool provides three functions along with visualization interfaces: (1) Rank user-generated predictions. (2) Provide an automated streamline of structure prediction and ranking for a given sequence. (3) Infer the functional aspects of a given structure. We demonstrated the applicability of SSRTool via real case studies and reported the similar trends between computed species-specific rankings and the corresponding prediction F1 values. The SSRTool web service is available online at https://cobisHSS0.im.nuk.edu.tw/SSRTool/, http://cosbi3.ee.ncku.edu.tw/SSRTool/, or the redirecting site https://github.com/cobisLab/SSRTool/.
RNA二级结构可以单独执行基本的细胞功能，或者相互作用形成分层的三级结构。实验性结构鉴定方法可以展示RNA分子的结构。然而，它们通常在分辨率上有限，并且成本高昂。因此，结构预测工具主要用于实验前分析。几十年来已经开发了各种结构预测模型。由于这些工具通常在了解实际RNA结构之前使用，在计算分析中对给定序列的一堆二级结构预测进行评估和排序至关重要。在本研究中，我们实现了一个名为SSRTool（RNA二级结构预测排名工具）的网络服务，以协助对给定序列生成的预测结构进行排名和评估。基于在四个常见RNA结构-功能方面计算出的物种特异性可解释性意义，SSRTool提供了三个功能以及可视化界面：（1）对用户生成的预测进行排名。（2）为给定序列提供结构预测和排名的自动化流程。（3）推断给定结构的功能方面。我们通过实际案例研究证明了SSRTool的适用性，并报告了计算出的物种特异性排名与相应预测F1值之间的相似趋势。SSRTool网络服务可在https://cobisHSS0.im.nuk.edu.tw/SSRTool/、http://cosbi3.ee.ncku.edu.tw/SSRTool/或重定向站点https://github.com/cobisLab/SSRTool/在线获取。
