COSMO: A dynamic programming algorithm for multicriteria codon optimization

Codon optimization in protein-coding sequences (CDSs) is a widely used technique to promote the heterologous expression of target genes. In codon optimization, a combinatorial space of nucleotide sequences that code a given amino acid sequence and take into account user-prescribed forbidden sequence motifs is explored to optimize multiple criteria. Although evolutionary algorithms have been used to tackle such complex codon optimization problems, evolutionary codon optimization tools do not provide guarantees to find the optimal solutions for these multicriteria codon optimization problems. We have developed a novel multicriteria dynamic programming algorithm, COSMO. By using this algorithm, we can obtain all Pareto-optimal solutions for the multiple features of CDS, which include codon usage, codon context, and the number of hidden stop codons. User-prescribed forbidden sequence motifs are rigorously excluded from the Pareto-optimal solutions. To accelerate CDS design by COSMO, we introduced constraints that reduce the number of Pareto-optimal solutions to be processed in a branch-and-bound manner. We benchmarked COSMO for run-time and the number of generated solutions by adapting selected human genes to yeast codon usage frequencies, and found that the constraints effectively reduce the run-time. In addition to the benchmarking of COSMO, a multi-objective genetic algorithm (MOGA) for CDS design was also benchmarked for the same two aspects and their performances were compared. In this comparison, (i) MOGA identified significantly fewer Pareto-optimal solutions than COSMO, and (ii) the MOGA solutions did not achieve the same mean hypervolume values as those provided by COSMO. These results suggest that generating the whole set of the Pareto-optimal solutions of the codon optimization problems is a difficult task for MOGA.