Ahmad Freed, Mahboob Shahid, Gulzar Tahsin, Din Salah U, Hanif Tanzeela, Ahmad Hifza, Afzal Muhammad
Department of Bioinformatics and Biotechnology, G C University, Faisalabad, Pakistan.
Bioinformation. 2013 Oct 16;9(17):873-8. doi: 10.6026/97320630009873. eCollection 2013.
The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.
RNA结构预测对于计算机模拟和体外研究中的进化理解都很有用。像核磁共振研究这样预测RNA二级结构的物理方法既昂贵又困难。计算RNA二级结构预测则更容易。比较序列分析提供了最佳解决方案。但是单个RNA序列的二级结构预测具有挑战性。RNA-SSPT是一种通过计算预测单个RNA序列二级结构的工具。大多数RNA二级结构预测工具不允许结构中存在假结，或者无法定位它们。Nussinov动态规划算法已在RNA-SSPT中实现。当前研究表明，只需要能量上最有利的二级结构，并且还可以进行算法修改以生成碱基对来降低二级结构的总自由能。为了可视化RNA二级结构，使用了C语言中的NAVIEW并在C#中针对工具需求进行了修改。RNA-SSPT是在Microsoft Visual Studio 2005专业版中使用Dot Net 2.0以C#构建的。RNA-SSPT的准确性通过灵敏度和阳性预测值进行了测试。它是一种兼具二级结构预测和二级结构可视化功能的工具。
