RT Journal Article
SR Electronic
T1 Optipyzer: A fast and flexible multi-species codon optimization server
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.05.22.541759
DO 10.1101/2023.05.22.541759
A1 LeRoy, Nathan
A1 Roleck, Caleigh
YR 2023
UL http://biorxiv.org/content/early/2023/05/24/2023.05.22.541759.abstract
AB 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.