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bioRxiv · 10.1101/2023.05.22.541759

Optipyzer: A fast and flexible multi-species codon optimization server

LeRoy, N. J.·Roleck, C.
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Abstract

Codon optimization is a commonly used tool in many fields of scientific research to optimize the expression profile of recombinant proteins in a target organism. It seeks to swap synonymous codons in a recombinant gene to reflect the specific codon usage bias of the expression system. While many tools for codon optimization exist, they cannot optimize a single gene for expression in multiple species and are typically limited in their ability to process large sets of genes. Additionally, these tools often only provide a single interface for running optimizations, making them incompatible with existing bioinformatics tools and pipelines. To address these shortcomings we created Optipyzer: an online codon optimization web server with an accompanying web interface and Python package for multi-species codon optimizations. Optipyzer was designed to be fast, flexible, and extensible - providing numerous interfaces for query submission. We believe that Optipyzer can be a powerful tool for the modern biologist by seamlessly integrating into any workflow. The main web interface can be accessed at https://optipyzer.com.

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LeRoy, N. J., Roleck, C.. 2023-05-24. Optipyzer: A fast and flexible multi-species codon optimization server. https://doi.org/10.1101/2023.05.22.541759

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