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Updated: Aug 12, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
CoDe: a web-based tool for codon deoptimization
Divya Sharma1, Tracey Baas2, Aitor Nogales3
1Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India.
Summary:
We have developed a web-based tool, CoDe (Codon Deoptimization) that deoptimizes genetic sequences based on different codon usage bias, ultimately reducing expression of the corresponding protein. The tool could also deoptimize the sequence for a specific region and/or selected amino acid(s). Moreover, CoDe can highlight sites targeted by restriction enzymes in the wild-type and codon-deoptimized sequences. Importantly, our web-based tool has a user-friendly interface with flexible options to download results.
Availability And Implementation:
The web-based tool CoDe is freely available at https://web.iitm.ac.in/bioinfo2/codeop/landing_page.html.
Supplementary Information:
Supplementary data are available at Bioinformatics Advances online.
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