Genetic algorithm for double digest problem

Abstract

The strongly NP-complete Double Digest Problem (DDP) for physical mapping of DNA, is now used for efficient genotyping. An instance of DDP has multiple distinct solutions. Existing methods produce a single solution, and are slow for large instances. We employ a type of equivalence among the distinct solutions to obtain almost all of them. Our method comprises of first finding a solution from each equivalence class by an elitist genetic algorithm, and then generating entire classes. Notable efficiency was achieved due to significant reduction in search space. © Springer-Verlag Berlin Heidelberg 2005.