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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,
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This repository contains simple CSV files (see[``data/tables/``](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/data/tables)) of the codon usage of various organisms,
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meant to be used by codon optimization software. All files in are of the form
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```
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etc.
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```
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It also contains a script to download new codon usage tables, using a TaxID to identify organisms.
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The data comes from [http://www.kazusa.or.jp](http://www.kazusa.or.jp) (they computed the codon usages from NCBI sequence data).
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More informations are available [here](http://www.kazusa.or.jp/codon/readme_codon.html
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Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
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```
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Python bindings
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---------------
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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.
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Language bindings
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-----------------
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This repositories also hosts the [python_codon_tables](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tree/master/python_codon_tables) package, which allows to use these tables from Python and download any new tables from Kazusa using taxonomic IDs.
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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.
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Contribute
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----------
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This repo was started at the Edinburgh Genome Foundry by Zulko and is released
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This repo was started at the Edinburgh Genome Foundry by [Zulko](https://github.com/Zulko) and is released
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on [Github](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables) 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.
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