A Self-Adaptive Cellular Memetic Algorithm for the DNA Fragment Assembly Problem

Abstract — The DNA fragment assembly problem is to re-construct a DNA chain from multiple fragments that have previously been sequenced in a laboratory. This is a critical step in any genomic project, since the resulting chains are the basis of all the work. Therefore, the quality of these chains is a prime importance to the correct development of the project. The methods typically applied to this problem usually encounter difficulties on large instances, so more efficient techniques are necessary. In this context, this work proposes a new method combining a general purpose metaheuristic (an advanced cellu-lar genetic algorithm which automatically regulates the intensity of the search) with a local search method specifically designed for this problem (PALS). This local search method (recently published) finds very accurate solutions in very short times. As a result, our proposal is a very accurate and efficient hybrid technique clearly outperforming the other existing ones. I