Longest Common Subsequence in k Length Substrings

In this paper we define a new problem, motivated by computational biology, LCSk aiming at finding the maximal number of k length substrings, matching in both input string while preserving their order of appearance in the input strings. The traditional LCS definition is a spacial case of our problem, where k = 1. We provide an algorithm, solving the general case in On 2 time, where n is the length of the input, equaling the time required for the special case of k = 1. The space requirement is Okn. In order to enable backtracking of the solution On 2 space is needed.

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