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A Practical Approximate Sub-Sequence Search Method for DNA Sequence Databases  

Won, Jung-Im (한양대학교 정보통신학부)
Hong, Sang-Kyoon (연세대학교 컴퓨터과학과)
Yoon, Jee-Hee (한림대학교 정보통신공학부)
Park, Sang-Hyun (연세대학교 컴퓨터과학과)
Kim, Sang-Wook (한양대학교 정보통신학부)
Publication Information
Journal of KIISE:Databases / v.34, no.2, 2007 , pp. 119-132 More about this Journal
Abstract
In molecular biology, approximate subsequence search is one of the most important operations. In this paper, we propose an accurate and efficient method for approximate subsequence search in large DNA databases. The proposed method basically adopts a binary trie as its primary structure and stores all the window subsequences extracted from a DNA sequence. For approximate subsequence search, it traverses the binary trie in a breadth-first fashion and retrieves all the matched subsequences from the traversed path within the trie by a dynamic programming technique. However, the proposed method stores only window subsequences of the pre-determined length, and thus suffers from large post-processing time in case of long query sequences. To overcome this problem, we divide a query sequence into shorter pieces, perform searching for those subsequences, and then merge their results. To verify the superiority of the proposed method, we conducted performance evaluation via a series of experiments. The results reveal that the proposed method, which requires smaller storage space, achieves 4 to 17 times improvement in performance over the suffix tree based method. Even when the length of a query sequence is large, our method is more than an order of magnitude faster than the suffix tree based method and the Smith-Waterman algorithm.
Keywords
DNA sequence database; approximate subsequence search; indexing; trie; suffix tree;
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