GADPO: Genetic Algorithm based on Dominance for Primer Optimization

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The amplification of the 16S ribosomal RNA gene through the polymerase chain reaction (PCR) is the main approach to profile bacterial communities. This gene is a widely used marker with a composition that allows the identification of microorganisms at the genus or species levels. The correct performance of a PCR assay depends on the properties of the chosen set of primers that match with the target 16S sequences, allowing the amplification by a DNA polymerase. For this reason, optimizing the design of primers attending to such multiple properties is crucial to ensure the specificity and robustness of this process. However, only one multiobjective proposal exists that addresses the optimization of primer design targeted to the 16S gene amplification. Herein, we propose a novel approach for multiobjective primer optimization based on a mutation-based genetic algorithm with three new problem-aware mutation operators, each aimed at covering one of the three objectives that compose the problem (efficiency, coverage, and variability). The proposed algorithm has been tested on 5 real datasets of bacterial 16S gene sequences. The results have been evaluated using 4 quality metrics, showing that our approach achieves statistically significant improvements with regard to the reference multiobjective approach in the field.