A practical method for approximate subsequence search in DNA databases
- Authors
- Won, Jung Im; Hong, Sang Kyoon; Yoon, Jee Hee; Park, Sanghyun; Kim, Sang Wook
- Issue Date
- May-2007
- Publisher
- Springer Verlag
- Keywords
- Approximate subsequence search; DNA database; Suffix tree
- Citation
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v.4426 LNAI, pp.921 - 931
- Indexed
- SCOPUS
- Journal Title
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
- Volume
- 4426 LNAI
- Start Page
- 921
- End Page
- 931
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/180122
- DOI
- 10.1007/978-3-540-71701-0_103
- ISSN
- 0302-9743
- Abstract
- 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.
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