CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.
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DOI：
10.1371/journal.pone.0147097
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Schlick T
中科院分区：
文献类型：
--
作者：
Hua L;Song Y;Kim N;Laing C;Wang JT;Schlick T
RNA连接是RNA分子的重要结构元素。当三个或更多的螺旋在三维空间中聚集在一起时，它们就形成了。近年来的研究主要集中在结内同轴螺旋叠加基序的注释和预测上。在这里，我们利用这种预测来开发一种有效的比对工具来处理具有CHS基序的RNA二级结构。具体来说，我们建立在我们的连接浏览器软件预测同轴叠加和RNAJAG建模连接拓扑作为树图，结合约束树匹配和动态规划算法到一个新的方法，称为CHSalign，对齐含有CHS基元RNA分子的二级结构。因此，CHSalign旨在成为含有类似连接的rna的有效比对工具。基于数千次比对的实验结果表明，CHSalign可以比其他RNA二级结构比对工具更准确地比对含有CHS基序的两个RNA二级结构。CHSalign在将两个具有相似CHS基序或螺旋排列模式的RNA二级结构对齐时得分较高，否则得分较低。这个新方法已经在一个web服务器上实现了，这个程序也可以在http://bioinformatics.njit.edu/CHSalign/上免费获得。
RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.