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June 2nd, 2025
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Weifang University of Science and Technology
bioinformatics
biorxiv

High-Codon: A Deep Learning-Based Codon Optimization Tool for Enhanced Heterologous Protein Expression in Escherichia coli

Li, J.Open in Google Scholar•Dong, X.Open in Google Scholar•Liu, J.Open in Google Scholar

High-Codon is a deep learning-based codon optimization tool designed to enhance the expression levels of heterologous proteins in Escherichia coli. This approach employs a BERT pre-trained model to construct a sequence labeling framework for predicting optimal codons. Additionally, an expression-level weighted loss function is introduced to strengthen the model's ability to learn from highly expressed proteins. Evaluation using 100 protein sequences from 34 species demonstrates that High-Codon outperforms traditional optimization methods.

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