edinburgh-genome-foundry / codon-usage-tables Goto Github PK

This repository contains simple CSV files (in data/tables/) of the codon usage of various organisms, meant to be used by codon optimization software. All files are in 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.

It also contains a script to download new codon usage tables, using a TaxID to identify organisms.

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.

To get these tables from Python, use the python_codon_tables package.

This repo was started at the Edinburgh Genome Foundry by Zulko and is released on Github into the Public Domain, and is also available under the CC0 license (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.