Gene sequences clustering for the prediction of functional domain = 기능 도메인 예측을 위한 유전자 서열 클러스터링

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Title
Gene sequences clustering for the prediction of functional domain = 기능 도메인 예측을 위한 유전자 서열 클러스터링
Author(s)
S I Han; S G Lee; Bo Kyeng Hou; Y S Byun; K S Hwang
Bibliographic Citation
Journal of Control, Automation, and Systems Engineering, vol. 12, no. 10, pp. 1044-1049
Publication Year
2006
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.
Keyword
clusteringgenemultiple sequence alignmentsequencesuffix treeBLASTdomain
ISSN
1225-9845
Publisher
South Korea
Type
Article
Appears in Collections:
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
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