shujun-he / codon-usage-tables

:bar_chart: Codon usage tables in code-friendly format + Python bindings

Codon usage tables for various organisms, in CSV format

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 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.

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.

Python bindings

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

Contribute

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.