Adaptation of harmony search algorithm for DNA fragment assembly problem

Abstract

DNA Fragment Assembly Problem (FAP) is an attractive research topic in the field of bioinformatics. The aim of DNA FAP is to generate DNA sequences as close to the original sequence among the given fragments. Various metaheuristic algorithms are applied to DNA Fragment Assembly Problem to find the best matching scores as well as the optimum fragment orders to obtain the original DNA sequence. In this paper, Harmony Search (HS) algorithm is adapted to DNA FAP by using Smallest Position Value (SPV) rule. SPV is used to convert continuous harmonics to the discrete orders of fragments. The algorithm is tested on three real DNA data sets to ensure its efficiency on FAP. Experimental results show that HS provides good matching scores and can be a good candidate for DNA fragment assembly problems.