An Integer Programming Formulation of the Minimum Common String Partition Problem

Abstract: We consider the problem of finding a minimum common string partition (MCSP) of two strings, which is an NP-hard problem. The MCSP problem is closely related to genome comparison and rearrangement, an important field in Computational Biology. In this paper, we map the MCSP problem into a graph applying a prior technique and using this graph, we develop an Integer Linear Programming (ILP) formulation for the problem. We implement the ILP formulation and compare the results with the state-of-the-art algorithms from the literature. The experimental results are found to be promising.