Tailoring codon usage to the underlying biology for protein expression 
optimization

Alirezaeizanjani, Zahra; Trösemeier, Jan-Hendrik; Kamp, Christel; Rudorf, Sophia

doi:10.1007/978-1-0716-1859-2_4

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Tailoring codon usage to the underlying biology for protein expression optimization

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Alirezaeizanjani, Zahra
Sophia Rudorf, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society;

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Rudorf, Sophia
Sophia Rudorf, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society;

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Citation

Alirezaeizanjani, Z., Trösemeier, J.-H., Kamp, C., & Rudorf, S. (2022). Tailoring codon usage to the underlying biology for protein expression optimization. In J. M. Walker (Ed.), Methods in Molecular Biology (pp. 85-92). New York, NY. doi:10.1007/978-1-0716-1859-2_4.

Cite as: https://hdl.handle.net/21.11116/0000-0009-EE5C-5

Abstract

For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced the software tool OCTOPOS. This sequence optimizer combines a detailed mechanistic mathematical modeling of in vivo protein synthesis with a state-of-the-art machine learning algorithm to find the sequence that best serves a user’s needs. Here, we briefly describe the algorithm and its implementation as well as its application in practice using OCTOPOS.