| A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences | |
Jia, Caiyan1; Lu, Ruqian2,3,4 ; Chen, Lusheng3,4
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| 2011-09-01 | |
| Source Publication | INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS
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| ISSN | 1875-6883 |
| Volume | 4Issue:5Pages:1032-1041 |
| Abstract | 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. |
| Keyword | Motif frequent pattern Apriori downward closure property |
| Language | 英语 |
| Funding Project | NSFC[60905029] ; NSFC[60875031] ; NSFC[90820013] ; 973 Project[2007CB311002] ; 973 Project[2009CB320701] |
| WOS Research Area | Computer Science |
| WOS Subject | Computer Science, Artificial Intelligence ; Computer Science, Interdisciplinary Applications |
| WOS ID | WOS:000297797300026 |
| Publisher | ATLANTIS PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/12071 |
| Collection | 数学所 |
| Corresponding Author | Jia, Caiyan |
| Affiliation | 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 |
| Recommended Citation 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. |
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