Approximation Algorithm for the Shortest Approximate Common Superstring Problem

The Shortest Approximate Common Superstring (SACS) problem is : Given a set of strings f={w1, w2, ... , wn}, where no wi is an approximate substring of wj, i ≠ j, find a shortest string Sa, such that, every string of f is an approximate substring of Sa. When the number of the strings n>2, the SACS problem becomes NP-complete. In this paper, we present a greedy approximation SACS algorithm. Our algorithm is a 1/2-approximation for the SACS problem. It is of complexity O(n2*(l2+log(n))) in computing time, where n is the number of the strings and l is the length of a string. Our SACS algorithm is based on computation of the Length of the Approximate Longest Overlap (LALO). Keywords—Shortest approximate common superstring, approximation algorithms, strings overlaps, complexities.