Journal of Institute of Control, Robotics and Systems (제어로봇시스템학회논문지)

Institute of Control, Robotics and Systems (제어로봇시스템학회)
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A Study on Clustering and Identifying Gene Sequences using Suffix Tree Clustering Method and BLAST

서픽스트리 클러스터링 방법과 블라스트를 통합한 유전자 서열의 클러스터링과 기능검색에 관한 연구

  • 한상일 (부산대학교 화학공학과) ;
  • 이성근 (부산대학교 화학공학과) ;
  • 김경훈 (부산대학교 화학공학과) ;
  • 이주영 (부산대학교 화학공학과) ;
  • 김영한 (동아대학교 화학공학과) ;
  • 황규석 (부산대학교 화학공학과)
  • Published : 2005.10.01
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Abstract

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

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References

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