Coder-friendly codon usage tables for various organisms, in CSV format
This repository contains simple CSV files (see
data/tables/) of the codon usage of various organisms,
meant to be used by codon optimization software. All files in are of the form
amino_acid,codon,relative_frequency *,UAA,0.64 *,UAG,0.07 *,UGA,0.29 A,GCA,0.21 A,GCC,0.27 K,AAA,0.76 K,AAG,0.24 etc.
The data comes from http://www.kazusa.or.jp (they computed the codon usages from NCBI sequence data).
More informations are available here and here is the original paper to cite:
Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
This repositories also hosts the python_codon_tables package, which allows to use these tables from Python and download any new tables from Kazusa using taxonomic IDs.
If you need these tables in another language, and you see a way to turn the repository into a package for that language, please submit a PR.
This repo was started at the Edinburgh Genome Foundry by Zulko and is released on Github under a Public Domain licence (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.