DNA Fragment Assembly Using Quantum-Inspired Genetic Algorithm

Abstract

DNA fragment assembly (DFA) is one of the most important and challenging problems in computational biology. DFA problem involves reconstruction of target DNA from several hundred (or thousands) of sequenced fragments by identifying the proper orientation and order of fragments. DFA problem is proved to be a NP-Hard combinatorial optimization problem. Metaheuristic techniques have the capability to handle large search spaces and therefore are well suited to deal with such problems. In this chapter, quantum-inspired genetic algorithm-based DNA fragment assembly (QGFA) approach has been proposed to perform the de novo assembly of DNA fragments using overlap-layout-consensus approach. To assess the efficacy of QGFA, it has been compared genetic algorithm, particle swarm optimization, and ant colony optimization-based metaheuristic approaches for solving DFA problem. Experimental results show that QGFA performs comparatively better (in terms of overlap score obtained and number of contigs produced) than other approaches considered herein.