Solving the Minimum Common String Partition Problem with the Help of Ants

In this paper, we consider the problem of finding a minimum common partition of two strings. The problem has its application in genome comparison. As it is an NPhard, discrete combinatorial optimization problem, we employ a metaheuristic technique, namely, MAX-MIN ant system to solve this problem. To achieve better efficiency we first map the problem instance into a special kind of graph. Subsequently, we employ a MAX-MIN ant system to achieve high quality solutions for the problem. Experimental results show the superiority of our algorithm in comparison with the state of art algorithm in the literature. The improvement achieved is also justified by standard statistical test. Keywords: Ant Colony Optimization, Stringology, Genome sequencing, Combinatorial Optimization, Swarm Intelligence, String partitioning 1. Introduction String comparison is one of the important problems in Computer Science with diverse applications in different areas including Genome Sequencing, text processing and compressions. In this paper, we address the problem of finding a minimum common partition (MCSP) of two strings. MCSP is closely related to genome arrangement which is an important topic in computational biology.