CHSalign：基于Junction-Explorer和RNAJAG的同轴螺旋堆叠RNA二级结构成对排列Web服务器
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking
摘要：
RNA连接是RNA分子的重要结构元件。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。最近的研究集中在注释和预测的同轴螺旋堆积（CHS）图案内的连接。在这里，我们利用这样的预测，开发一个有效的比对工具来处理RNA二级结构与CHS基序。具体来说，我们建立在我们的连接，资源管理器软件预测同轴堆叠和RNAJAG建模连接拓扑结构的树形图，将约束树匹配和动态规划算法到一个新的方法，称为CHSalign，对齐的二级结构的RNA分子含有CHS基序。因此，CHSalign旨在成为包含相似连接的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。当比对具有相似CHS基序或螺旋排列模式的两个RNA二级结构时，CHSalign产生高分，否则产生低分。这种新方法已经在Web服务器中实现，该程序也可以在http://bioinformatics.njit.edu/CHSalign/上免费获得。
英文摘要：
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/.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
