A Local-stem-search Algorithm to Predict The RNA Secondary Structure

doi:10.3724/SP.J.1206.2009.00329

	A Local-stem-search Algorithm to Predict The RNA Secondary Structure
	Chen Xiang 2,3,4; Bu Dong-Bo 2,3; Zhang Fa 1,2,3; Gao Wen 1
	2009
发表期刊	PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
ISSN	1000-3282
卷号	36 期号:1 页码:115-121
摘要	RNA secondary structure predicting is a classical problem in bioinformatics and the optimal algorithms based on minimal free energy (WE) criterion are the widely used methods. However, pseudoknots render the problem of computing the RNA MFE structure with pseudoknot becomes a NP-hard problem. A heuristic algorithm-StemFind to predict RNA secondary structure with pseudoknot was presented. The algorithm regard stem as the basic search unit, adopting heuristic search strategy, and search the most possible RNA secondary structure in stem combination space. The StemFind algorithm to a large number of test sets was applied. Performance evaluation demonstrates that StemFind not only outperforms the well-known optimal and heuristic algorithms in overall sensitivity and specificity but also requires significantly less time than the optimal algorithm.
关键词	RNA secondary structure prediction pseudoknot NP-hard heuristic algorithm
DOI	10.3724/SP.J.1206.2009.00329
收录类别	SCI
语种	英语
资助项目	National Basic Research Program of China[2002CB713807] ; Frontier Project of Knowledge Innovation Program of The Chinese Academy of Sciences[20076020] ; The National Natural Science Foundation of China[60503060] ; The National Natural Science Foundation of China[90612019] ; The National Natural Science Foundation of China[60752001]
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemistry & Molecular Biology ; Biophysics
WOS记录号	WOS:000262626200016
出版者	CHINESE ACAD SCIENCES, INST BIOPHYSICS
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11828
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Gao Wen
作者单位	1.Peking Univ, Sch Elect Engn & Comp Sci, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Comp Technol Inst, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Chen Xiang,Bu Dong-Bo,Zhang Fa,et al. A Local-stem-search Algorithm to Predict The RNA Secondary Structure[J]. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,2009,36(1):115-121.
APA	Chen Xiang,Bu Dong-Bo,Zhang Fa,&Gao Wen.(2009).A Local-stem-search Algorithm to Predict The RNA Secondary Structure.PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,36(1),115-121.
MLA	Chen Xiang,et al."A Local-stem-search Algorithm to Predict The RNA Secondary Structure".PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 36.1(2009):115-121.