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Gene Sequences Clustering and Identifying Functional Domain Using a Suffix Tree Algorithm

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4 Author(s)
Sang Il Han ; Department of Chemical Engineering, Pusan National University, Busan 609-735, Korea. Tel : +82-51-510-2400; E-mail: ; Sung Gun Lee ; Kyu Suk Hwang ; Young Han Kim

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment by pairwise alignment. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria, identifying 11 clusters

Published in:

2006 SICE-ICASE International Joint Conference

Date of Conference:

18-21 Oct. 2006