Efficient algorithms for finding interleaving relationship between sequences

Authors:
Kuo-Si Huang;Chang-Biau Yang;Kuo-Tsung Tseng;Hsing-Yen Ann;Yung-Hsing Peng
Affiliations:
Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
Venue:
Information Processing Letters
Year:
2008

Citing 10
Cited 3

Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology
All Highest Scoring Paths in Weighted Grid Graphs and Their Application to Finding All Approximate Repeats in Strings

SIAM Journal on Computing
The Complexity of Some Problems on Subsequences and Supersequences

Journal of the ACM (JACM)
A linear space algorithm for computing maximal common subsequences

Communications of the ACM
On the common substring alignment problem

Journal of Algorithms
Sparse LCS common substring alignment

Information Processing Letters
A simple algorithm for the constrained sequence problems

Information Processing Letters
Dynamic programming algorithms for the mosaic longest common subsequence problem

Information Processing Letters
Two algorithms for LCS Consecutive Suffix Alignment

Journal of Computer and System Sciences
A fast algorithm for computing a longest common increasing subsequence

Information Processing Letters

Efficient change control of XML documents

Proceedings of the 9th ACM symposium on Document engineering
Efficient algorithms for the block edit problems

Information and Computation
Efficient algorithms for the longest common subsequence problem with sequential substring constraints

Journal of Complexity

Quantified Score

Hi-index	0.89

Visualization

Abstract

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(n^3) 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(n^2m), where m is the number of blocks. An improved O(n^2+nm^2) algorithm is further proposed for the same blocked problem.