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arXiv · 1311.4552

Efficient algorithms for the longest common subsequence in $k$-length substrings

Sebastian Deorowicz·Szymon Grabowski
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Abstract

Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences $A$ and $B$ are replaced with matching non-overlapping substrings of length $k$ from $A$ and $B$. We propose several algorithms for LCS$k$, being non-trivial incarnations of the major concepts known from LCS research (dynamic programming, sparse dynamic programming, tabulation). Our algorithms make use of a linear-time and linear-space preprocessing finding the occurrences of all the substrings of length $k$ from one sequence in the other sequence.

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Sebastian Deorowicz, Szymon Grabowski. 2013-11-18. Efficient algorithms for the longest common subsequence in $k$-length substrings. https://arxiv.org/abs/1311.4552

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