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Title 

Gene sequences clustering for the prediction of functional domain

 

기능 도메인 예측을 위한 유전자 서열 클러스터링

Authors 

S I HanS G LeeBo Kyeng HouY S ByunK S Hwang

Publisher 

Elsevier

Issue Date 

2006

Citation 

Journal of Control, Automation, and Systems Engineering, vol. 12, no. 10, pp. 1044-1049

Keywords 

clusteringgenemultiple sequence alignmentsequencesuffix treeBLASTdomain

Abstract 

Multiple sequence alignment is a method for comparing two or more DNA or protein sequences. Most multiple sequence alignment methods rely on pairwise alignment and Smith-Waterman algorithm [Needleman and Wunsch, 1970; Smith and Waterman, 1981] to generate an alignment hierarchy. Therefore, as the number of sequences increases, the runtime increases exponentially. To resolve this problem, this paper presents a multiple sequence alignment method using a parallel processing suffix tree algorithm to search for common subsequences at one time without pairwise alignment. The cross-matched subsequences among the searched common subsequences may be generated and those cause inexact-matching. So the procedure of masking cross-matching pairs was suggested in this study. The proposed method, improved STC (Suffix Tree Clustering), is summarized as follows: (1) construction of suffix tree; (2) search and overlap of common subsequences; (3) grouping of subsequence pairs; (4) masking of cross-matching pairs; and (5) clustering of gene sequences. The new method was successfully evaluated with 23 genes in Mus musculus and 22 genes in three species, clustering nine and eight clusters, respectively.

Citation 

ISSN 

1225-9845

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2017-04-19


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