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2008

Efficient algorithms for finding interleaving relationship between sequences

9 years 6 months ago
Efficient algorithms for finding interleaving relationship between sequences
The longest common subsequence and sequence alignment problems have been studied extensively and they can be regarded as the relationship measurement between sequences. However, most of them treat sequences evenly or consider only two sequences. Recently, with the rise of whole-genome duplication research, the doubly conserved synteny relationship among three sequences should be considered. It is a brand new model to find a merging way for understanding the interleaving relationship of sequences. Here, we define the merged LCS problem for measuring the interleaving relationship among three sequences. An O(n3) algorithm is first proposed for solving the problem, where n is the sequence length. We further discuss the variant version of this problem with the block information. For the blocked merged LCS problem, we propose an algorithm with time complexity O(n2m), where m is the number of blocks. An improved O(n2 + nm2) algorithm is further proposed for the same blocked problem.
Kuo-Si Huang, Chang-Biau Yang, Kuo-Tsung Tseng, Hs
Added 12 Dec 2010
Updated 12 Dec 2010
Type Journal
Year 2008
Where IPL
Authors Kuo-Si Huang, Chang-Biau Yang, Kuo-Tsung Tseng, Hsing-Yen Ann, Yung-Hsing Peng
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