Optimization of designing multiple genes encoding the same protein based on NSGA-II for efficient execution on GPUs

In synthetic biology, it is a challenge to increase the production of target proteins by maximizing their expression levels. In order to augment expression levels, we need to focus on both homologous recombination and codon adaptation, which are estimated by three objective functions, namely HD (Hamming distance), LRCS (length of repeated or common substring) and CAI (codon adaptation index). Optimizing these objective functions simultaneously becomes a multi-objective optimization problem. The aim is to find satisfying solutions that have high codon adaptation and a low incidence of homologous recombination. However, obtaining satisfactory solutions requires calculating the objective functions multiple times with many cycles and solutions. In this paper, we propose an approach to accelerate the method of designing a set of CDSs (CoDing sequences) based on NSGA-II (non-dominated sorting genetic algorithm II) on NVIDIA GPUs. The implementation accelerated by GPUs improves overall performance by 187.5 $\times$ using $100$ cycles and $128$ solutions. Our implementation allows us to use larger solutions and more cycles, leading to outstanding solution quality. The improved implementation provides much better solutions in a similar amount of time compared to other available methods by 1.22 $\times$ improvements in hypervolume. Furthermore, our approach on GPUs also suggests how to efficiently utilize the latest computational resources in bioinformatics. Finally, we discuss the impacts of the number of cycles and the number of solutions on designing a set of CDSs.