An Algorithm for a Variation of the Shortest Common Superstring Problem

TL;DR

This paper introduces an exact algorithm for a modified Shortest Common Superstring problem allowing for errors and non-substring constraints, advancing solutions for complex string assembly tasks.

Contribution

It presents the first exact algorithm addressing a variation of the SCS problem with error tolerance and substring restrictions.

Findings

Algorithm effectively handles K-mistake tolerance.

Proven optimal solutions for the modified problem.

Applicable to complex string assembly scenarios.

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.