Codon usage optimization is a method for replacing synonymous codons in order to adapt the codon usage of the host organism. It is used in the preparation of protein synthesis, e.g. in the production of drugs, food industry additives, or in the study of protein properties in the laboratory.
Suboptimal codon usage leads to a low expression efficiency, improper protein folding, and consequently, an unusable final product. Hence, optimization is a crucial step in the preparation of synthetic proteins.
We have designed and implemented a web application for real-time interactive codon optimization based on translation time simulation.
Multiple algorithms for codon usage optimization were designed, implemented, and compared.
The application relies on the RTA* algorithm with a depth of 1, achieving a 55% +/- 5% improvement in relative error. It encompasses the entire sequence preparation process for structure-based protein optimization.
We presented the application to target users and assessed their response through a questionnaire.
Based on this 91% of users believe that the user interface meets all their requirements for codon optimization. More than two-thirds of respondents find the algorithm execution sufficiently fast. All respondents expressed interest in using the algorithm's results in their work.
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