Metaheuristic Assemblers of DNA strands: Noiseless and Noisy Cases

The DNA fragment assembly problem is an NP-complete problem which has been solved efficiently by many metaheuristics. However, those techniques generally assemble fragments that belong to noiseless DNA sequences. But nowadays dealing with noisy instances is imperative. For that we analyse exhaustively how noiseless and noisy instances of this problem are dealt by three efficient algorithms (Problem aware local search, Simulated Annealing and Genetic Algorithims). This analysis includes a performance evaluation of those algorithms to assemble fragments and a study of the solution composition. From these analysis we observe that the GA is more robust in presence of noise than the other two searches, while it usually does not improve the accuracy of results for large instances (where Simulated Annealing is the more precise technique).