{"id":21466713,"url":"https://github.com/Edinburgh-Genome-Foundry/python_codon_tables","last_synced_at":"2026-01-09T23:05:16.181Z","repository":{"id":45283054,"uuid":"80102005","full_name":"Edinburgh-Genome-Foundry/codon-usage-tables","owner":"Edinburgh-Genome-Foundry","description":":bar_chart: Codon usage tables in code-friendly format + Python bindings","archived":false,"fork":false,"pushed_at":"2025-01-27T16:48:54.000Z","size":61,"stargazers_count":36,"open_issues_count":0,"forks_count":10,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-03-21T18:01:08.179Z","etag":null,"topics":["bioinformatics","codon-optimization","codon-usage","synbio"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Edinburgh-Genome-Foundry.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-01-26T09:46:32.000Z","updated_at":"2025-03-19T15:50:25.000Z","dependencies_parsed_at":"2025-02-15T14:13:36.560Z","dependency_job_id":"2edb1982-87d6-4d88-ae8b-3853ad7e83c6","html_url":"https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fcodon-usage-tables","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fcodon-usage-tables/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fcodon-usage-tables/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Edinburgh-Genome-Foundry%2Fcodon-usage-tables/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Edinburgh-Genome-Foundry","download_url":"https://codeload.github.com/Edinburgh-Genome-Foundry/codon-usage-tables/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246085594,"owners_count":20721210,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","codon-optimization","codon-usage","synbio"],"created_at":"2024-11-23T08:15:01.460Z","updated_at":"2026-01-09T23:05:16.150Z","avatar_url":"https://github.com/Edinburgh-Genome-Foundry.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Codon usage tables for various organisms, in CSV format\n-------------------------------------------------------\n\nThis 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,\nmeant to be used by codon optimization software. All files are in the form\n\n```\namino_acid,codon,relative_frequency\n*,UAA,0.64\n*,UAG,0.07\n*,UGA,0.29\nA,GCA,0.21\nA,GCC,0.27\nK,AAA,0.76\nK,AAG,0.24\netc.\n```\n\nIt also contains a script to download new codon usage tables, using a TaxID to identify organisms.\n\nThe data comes from [http://www.kazusa.or.jp](http://www.kazusa.or.jp) (they computed the codon usages from NCBI sequence data).\n\nMore information is available [here](http://www.kazusa.or.jp/codon/readme_codon.html\n) and here is the original paper to cite:\n\n```\nCodon usage tabulated from the international DNA sequence databases: status for the year 2000.\nNakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.\n```\n\nPython bindings\n---------------\n\nTo 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.\n\nContribute\n----------\n\nThis 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FEdinburgh-Genome-Foundry%2Fpython_codon_tables","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FEdinburgh-Genome-Foundry%2Fpython_codon_tables","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FEdinburgh-Genome-Foundry%2Fpython_codon_tables/lists"}