Prediction for RNA planar pseudoknots  

作　　者：Li Hengwu Zhu Daming Liu Zhendong Li Hong 

机构地区：[1]School of Computer Science and Technology, Shandong University, Jinan 250100, China [2]Department of Computer, ShandongEconomic University, Jinan 250014, China

出　　处：《Progress in Natural Science:Materials International》2007年第6期717-724,共8页自然科学进展·国际材料（英文版）

基　　金：Supported by National Natural Science Foundation of China (Grant Nos 60573024 and 60573181);the Research Project of Shandong EconomicUniversity (01610784);NSF of Shandong Provice (2005BS01014)

摘　　要：Based on m-stems and semi-extensible structure, a model is presented to represent RNA planar pseudoknots, and corresponding dynamic programming algorithm is designed and implemented to predict arbitrary planar pseudoknots and simple non-planar pseudoknots with O(n4) time and O(n3) space. The algorithm folds total 245 sequences in the Pseudobase database, and the test results indicate that the algorithm has good accuracy, sensitivity and specificity.Based on m-stems and semi-extensible structure, a model is presented to represent RNA planar pseudoknots, and corresponding dynamic programming algorithm is designed and implemented to predict arbitrary planar pseudoknots and simple non-planar pseudoknots with O （n^4） time and O （n^3） space. The algorithm folds total 245 sequences in the Pseudobase database, and the test results indicate that the algorithm has good accuracy, sensitivity and specificity.

关 键 词：ALGORITHM RNA secondary structure PSEUDOKNOT dynamic programming 

分 类 号：Q522[生物学—生物化学]