{"id":23051451,"url":"https://github.com/averissimo/orf_finder","last_synced_at":"2025-07-01T05:39:53.599Z","repository":{"id":56887012,"uuid":"49449677","full_name":"averissimo/orf_finder","owner":"averissimo","description":"Finds the longest orfs in a nucleotide sequence.","archived":false,"fork":false,"pushed_at":"2016-06-24T14:19:56.000Z","size":30,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-06-03T07:01:18.981Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Ruby","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/averissimo.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}},"created_at":"2016-01-11T19:41:00.000Z","updated_at":"2024-02-01T13:37:26.000Z","dependencies_parsed_at":"2022-08-20T13:50:05.754Z","dependency_job_id":null,"html_url":"https://github.com/averissimo/orf_finder","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/averissimo/orf_finder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Forf_finder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Forf_finder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Forf_finder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Forf_finder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/averissimo","download_url":"https://codeload.github.com/averissimo/orf_finder/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/averissimo%2Forf_finder/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262906063,"owners_count":23382725,"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":[],"created_at":"2024-12-15T23:45:56.895Z","updated_at":"2025-07-01T05:39:53.575Z","avatar_url":"https://github.com/averissimo.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ORF-Finder\n\n**Website**: [http://sels.tecnico.pt/orf_finder](http://sels.tecnico.pt/orf_finder/)\n\nORF-Finder is a library that finds the longest Open Reading Frame (ORF) from a nucleotide sequence.\n\nIt will search the sequence for existing start and stop codons and return a single ORF for each frame.\n\nWhen there is not a ORF present with any of the configurated start and stop codons, then it fallbacks to:\n - Using the first codon of the sequence when:\n   - No start codon is present;\n   - The lenght of an ORF is shorter than the minimum option;\n - Using the last codon of the sequence when:\n   - No stop codon is present.\n\nnote: this was developed in parallell with [mass-blast](http://github.com/averissimo/mass-blast) and due to the lack of a Ruby library that had this functionality.\n\n# Installation\n\nORF-Finder can be installed from RubyGems.org by:\n\n    gem install orf_finder\n\nor adding to the [Gemfile](http://bundler.io/gemfile.html):\n\n    gem 'orf_finder'\n\nor adding directly from the github repository:\n\n    gem 'orf_finder', github: 'averissimo/orf_finder'\n\n# Usage\n\nThere are two classes that can be used to search for ORF,\n  - ORFinder: can look at both the direct sequence or the complement.\n\n        my_orf = ORFFinder.new('aaaatgaaaaaaatgtaaaaa', min: 3)\n        my_orf.nt # returns the longests ORFs for all reading frames as a nucleotide sequence, both the direct and complement\n        my_orf.nt # returns the longests ORFs for all reading frames as an amino-acid sequence, both the direct and complement\n\n\n  - ORF: only looks at the direct string.\n\n        my_orf = ORF.new('aaaatgaaaaaaatgtaaaaa', min: 3)\n        my_orf.nt # returns the longests ORFs for all reading frames as a nucleotide sequence, both the direct and complement\n        my_orf.nt # returns the longests ORFs for all reading frames as an amino-acid sequence, both the direct and complement\n\n\n# Options\n\n- 'start': list of strings\n  - Defines the allowed start codons\n- 'stop': list of strings\n  - Defines the allowed stop codons\n- 'reverse': true/false\n  - Whether it should look at the complement\n- 'direct': true/false\n  - Whether it should look at the direct sequence (as is)\n- 'min': integer\n  - Minimum length for an ORF to be considered\n- 'debug': true/false\n  - Whether or not to create an log file\n\n# Ackowledgements\n\n  This tool was created as a part of [FCT](www.fct.p) grant SFRH/BD/97415/2013 and European Commission research project [BacHBerry](www.bachberry.eu) (FP7- 613793)\n\n  [Developer](http://web.tecnico.ulisboa.pt/andre.verissimo/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faverissimo%2Forf_finder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faverissimo%2Forf_finder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faverissimo%2Forf_finder/lists"}