https://github.com/edinburgh-genome-foundry/codon-usage-tables

:bar_chart: Codon usage tables in code-friendly format + Python bindings
https://github.com/edinburgh-genome-foundry/codon-usage-tables

bioinformatics codon-optimization codon-usage synbio

Last synced: 3 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/codon-usage-tables
• Owner: Edinburgh-Genome-Foundry
• License: cc0-1.0
• Created: 2017-01-26T09:46:32.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2022-05-05T16:29:43.000Z (over 2 years ago)
• Last Synced: 2024-12-06T15:52:43.182Z (16 days ago)
• Topics: bioinformatics, codon-optimization, codon-usage, synbio
• Language: Python
• Homepage:
• Size: 56.6 KB
• Stars: 35
• Watchers: 7
• Forks: 9
• Open Issues: 1
• 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 informations are 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.