A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences

CSpace > 数学所

	A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences
	Jia, Caiyan 1; Lu, Ruqian2,3,4 ; Chen, Lusheng 3,4
	2011-09-01
发表期刊	INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS
ISSN	1875-6883
卷号	4 期号:5 页码:1032-1041
摘要	Identification and characterization of gene regulatory binding motifs is one of the fundamental tasks toward systematically understanding the molecular mechanisms of transcriptional regulation. Recently, the problem has been abstracted as the challenge planted (l,d)-motif problem. Previous studies have developed numerous methods to solve the problem. But most of them need to specify the length l of a planted motif in advance and use depth first search strategy. In this study, we present an exact and efficient algorithm, called Apriori-Motif, without given the length l of a planted motif a priori. And a breadth first search strategy is used to prune search space quickly by the downward closure property utilized in Apriori, which is a classical algorithm for frequent pattern mining. Empirical study shows that Apriori-Motif is better than some existing methods.
关键词	Motif frequent pattern Apriori downward closure property
语种	英语
资助项目	NSFC[60905029] ; NSFC[60875031] ; NSFC[90820013] ; 973 Project[2007CB311002] ; 973 Project[2009CB320701]
WOS研究方向	Computer Science
WOS类目	Computer Science, Artificial Intelligence ; Computer Science, Interdisciplinary Applications
WOS记录号	WOS:000297797300026
出版者	ATLANTIS PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/12071
专题	数学所
通讯作者	Jia, Caiyan
作者单位	1.Beijing Jiaotong Univ, Dept Comp Sci, Beijing 100044, Peoples R China 2.Chinese Acad Sci, Inst Math, Beijing 100080, Peoples R China 3.Fudan Univ, Shanghai Key Lab Intelligent Informat Proc, Shanghai 200433, Peoples R China 4.Fudan Univ, Dept Comp Sci & Engn, Shanghai 200433, Peoples R China
推荐引用方式 GB/T 7714	Jia, Caiyan,Lu, Ruqian,Chen, Lusheng. A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences[J]. INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS,2011,4(5):1032-1041.
APA	Jia, Caiyan,Lu, Ruqian,&Chen, Lusheng.(2011).A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences.INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS,4(5),1032-1041.
MLA	Jia, Caiyan,et al."A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences".INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS 4.5(2011):1032-1041.