An Algorithm for a Variation of the Shortest Common Superstring Problem

Abstract

This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not matching the SCS in at most K positions. Second, no string in S can be a substring of another in S. The algorithm proposed for the problem is exact.