The longest common subsequence problem for small alphabet size between many strings

Abstract

Given two or more strings (for example, DNA and amino acid sequences), the longest common subsequence (LCS) problem is to determine the longest common subsequence obtained by deleting zero or more symbols from each string. The algorithms for computing an LCS between two strings were given by many papers, but there is no efficient algorithm for computing an LCS between more than two strings. This paper proposes a method for computing efficiently the LCS between three or more strings of small alphabet size. Specifically, our algorithm computes the LCS of d(≥ 3) strings of length n on alphabet of size s in O(usd + Dsd(logd-3n + logd-2s)) time, where D is the number of dominant matches and is much smaller than nd. Through computational experiments, we demonstrate the effectiveness of our algorithm.