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Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks
Liu, DR; Xiong, XX; Hou, ZG; DasGupta, B
Source PublicationNEURAL NETWORKS
2005-06-01
Volume18Issue:5-6Pages:835-842
SubtypeArticle
AbstractThe problem of motif identification in protein sequences has been studied for many years in the literature. Current popular algorithms of motif identification in protein sequences face two difficulties, high computational cost and the possibility of insertions and deletions. In this paper, we provide a new strategy that solve the problem more efficiently. We develop a self-organizing neural network structure with multiple levels of subnetworks to make an intelligent classification of the subsequences obtained from protein sequences. We maintain a low computational complexity through the use of this multi-level structure so that the classification of each subsequence is performed with respect to a small subspace of the whole input space. The new definition of pairwise distance between motif patterns provided in this paper can deal with up to two insertions/deletions allowed in a motif, while other existing algorithm can only deal with one insertion or deletion. We also maintain a high reliability using our self-organizing neural network since it will grow as needed to make sure all input patterns are considered and are given the same amount of attention. Simulation results show that our algorithm significantly outperforms existing algorithms in both accuracy and reliability aspects. (c) 2005 Elsevier Ltd. All rights reserved.
KeywordDna Motif Identification Multiple Sequence Alignment Neural Network Self-organization
WOS HeadingsScience & Technology ; Technology
WOS KeywordALIGNMENT
Indexed ByISTP ; SCI
Language英语
WOS Research AreaComputer Science
WOS SubjectComputer Science, Artificial Intelligence
WOS IDWOS:000232096500044
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ia.ac.cn/handle/173211/9086
Collection09年以前成果
Affiliation1.Univ Illinois, Dept Elect & Comp Engn, Chicago, IL 60607 USA
2.Chinese Acad Sci, Key Lab Complex Syst & Intelligence Sci, Beijing, Peoples R China
3.Univ Illinois, Dept Comp Sci, Chicago, IL USA
Recommended Citation
GB/T 7714
Liu, DR,Xiong, XX,Hou, ZG,et al. Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks[J]. NEURAL NETWORKS,2005,18(5-6):835-842.
APA Liu, DR,Xiong, XX,Hou, ZG,&DasGupta, B.(2005).Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks.NEURAL NETWORKS,18(5-6),835-842.
MLA Liu, DR,et al."Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks".NEURAL NETWORKS 18.5-6(2005):835-842.
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