Using Folding Ensemble and Stem Probability Maximization Methods to Predict RNA H-Type Pseudoknots  

作　　者：Junilda Spirollari Shawn Xiong Wang Jason T.L. Wang 

机构地区：[1]Bioinformatics Program, Department of Computer Science, New Jersey Institute of Technology, University Heights [2]Department of Computer Science, California State University

出　　处：《Tsinghua Science and Technology》2012年第6期691-700,共10页清华大学学报（自然科学版（英文版）

摘　　要：We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at http：//bioinformatics.njit.edu/KnotFold.We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at http：//bioinformatics.njit.edu/KnotFold.

关 键 词：RNA structure PSEUDOKNOTS tool ensemble 

分 类 号：Q522[生物学—生物化学]