"Optimization in Sanger sequencing"
Silvia Lorenzo-Freire, Luisa Carpente, Ana Cerdeira-Pena and Ángeles S. Places

The main objective of this paper is to solve the optimization problem that is associated with classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model that can only be solved for small instances. Since it is necessary to find feasible and reasonable solutions to the problem for real instances, which involve the classification of thousands of samples, we also propose a heuristic algorithm based on the simulated annealing technique. This algorithm obtains satisfactory solutions in a short amount of time. It has been tested with real data and yields improved results compared to the software that was previously used in the laboratory. Moreover, the algorithm has already been implemented in the laboratory and is being successfully used.