Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.

ABSTRACT: Codon optimization is an essential technique in synthetic biology and biopharmaceutical production, enhancing recombinant protein expression by fine-tuning genetic sequences to match the translational machinery and codon usage preferences of specific host organisms. This study presents a comprehensive comparative analysis of widely used codon optimization tools, focusing on their capacity to reflect host-specific codon biases, design principles, and parameters. Industrially relevant target proteins were evaluated in Escherichia coli, Saccharomyces cerevisiae, and CHO cells, uncovering significant variability in sequence design and clustering patterns across tools. Tools such as JCat, OPTIMIZER, ATGme, and GeneOptimizer demonstrated strong alignment with genome-wide and highly

SUBMITTER: Demissie EA 

PROVIDER: S-EPMC12010093 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature