https://github.com/Edinburgh-Genome-Foundry/python_codon_tables
:bar_chart: Codon usage tables in code-friendly format + Python bindings
https://github.com/Edinburgh-Genome-Foundry/python_codon_tables
bioinformatics codon-optimization codon-usage synbio
Last synced: 25 days ago
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:bar_chart: Codon usage tables in code-friendly format + Python bindings
- Host: GitHub
- URL: https://github.com/Edinburgh-Genome-Foundry/python_codon_tables
- Owner: Edinburgh-Genome-Foundry
- License: cc0-1.0
- Created: 2017-01-26T09:46:32.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2025-01-27T16:48:54.000Z (about 1 year ago)
- Last Synced: 2025-03-21T18:01:08.179Z (11 months ago)
- Topics: bioinformatics, codon-optimization, codon-usage, synbio
- Language: Python
- Homepage:
- Size: 59.6 KB
- Stars: 36
- Watchers: 6
- Forks: 10
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Codon usage tables for various organisms, in CSV format
-------------------------------------------------------
This repository contains simple CSV files (in [``data/tables/``](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/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](http://www.kazusa.or.jp) (they computed the codon usages from NCBI sequence data).
More information is available [here](http://www.kazusa.or.jp/codon/readme_codon.html
) 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](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/python_codon_tables) package.
Contribute
----------
This repo was started at the Edinburgh Genome Foundry by Zulko and is released on [Github](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables) into the Public Domain, and is also available under the [CC0 license](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.