{"id":26573245,"url":"https://github.com/linsalrob/repeatfinder","last_synced_at":"2025-03-23T00:39:55.307Z","repository":{"id":234360878,"uuid":"788740798","full_name":"linsalrob/repeatfinder","owner":"linsalrob","description":"fast code for searching for direct and indirect repeats in DNA sequences.","archived":false,"fork":false,"pushed_at":"2024-06-12T01:53:00.000Z","size":104,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-06-12T13:09:36.022Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linsalrob.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citation.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-04-19T01:49:53.000Z","updated_at":"2024-06-12T01:53:03.000Z","dependencies_parsed_at":null,"dependency_job_id":"2b0d8d7d-147a-440c-a3c9-c24368e4aa4b","html_url":"https://github.com/linsalrob/repeatfinder","commit_stats":null,"previous_names":["linsalrob/repeatfinder"],"tags_count":15,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Frepeatfinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Frepeatfinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Frepeatfinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Frepeatfinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linsalrob","download_url":"https://codeload.github.com/linsalrob/repeatfinder/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040190,"owners_count":20551299,"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":"2025-03-23T00:39:54.870Z","updated_at":"2025-03-23T00:39:55.295Z","avatar_url":"https://github.com/linsalrob.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.sdsu.edu/research)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![GitHub language count](https://img.shields.io/github/languages/count/linsalrob/repeat_finder)\n[![DOI](https://zenodo.org/badge/788740798.svg)](https://zenodo.org/doi/10.5281/zenodo.11565325)\n\n# Repeat Finder - Finding Repeats in DNA sequences\n\nRepeatfinder is a stand alone program to quickly find repeats in DNA sequences. You might find that it is remarkably similar to an essential module in [PhiSpy](http://github.com/linsalrob/PhiSpy).\n\n# How to find repeats\n\n\n## Using the command line\nYou can use the `pydna_repeatfinder` command to find repeats in a fasta sequence.\n\nBy default, `pydna_repeatfinder` just prints the repeats in a `simple` tab-separated format that is easy to read and includes the DNA sequence.\n\nFor example:\n\n```\n$ pydna_repeatfinder -f tests/test_long.fasta\nrandom_sequence Number:1        Len1:52 Len2:52 92      144     1946    1998    TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT    TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT\nrandom_sequence Number:2        Len1:52 Len2:52 92      144     197     145     TCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT    CACCGTATACTCCATACTTCCGCGATACCCTTAGGCTAACCTACGACAACTG\nrandom_sequence Number:3        Len1:53 Len2:53 145     198     1998    1945    CACCGTATACTCCATACTTCCGCGATACCCTTAGGCTAACCTACGACAACTGA   ATCAGTTGTCGTAGGTTAGCCTAAGGGTATCGCGGAAGTATGGAGTATACGGT\n```\n\nThere are two long repeats here. The first from 92-144 is repeated in the same orientation (a direct repeat) at position 1946-1998.\n\nWe can also output the results formated so you can paste them directly into a GenBank file. This is perhaps the easiest way to visualise the repeats.\n\n```\n$ pydna_repeatfinder -f tests/test_long.fasta -o genbank\n     repeat_region   join(92..144,1946..1998)\n                     /note=\"direct repeat number 1 of length 53\"\n                     /rpt_type=\"direct\"\n     repeat_region   join(92..144,complement(197..145))\n                     /note=\"inverted repeat number 2 of length 53\"\n                     /rpt_type=\"inverted\"\n     repeat_region   join(145..198,complement(1998..1945))\n                     /note=\"inverted repeat number 3 of length 54\"\n                     /rpt_type=\"inverted\"\n```\n\n## In your own code\n\nYou can import the `pydna_repeatfinder` module and use it in your own code:\n\n\n```\nfrom PyRepeatFinder import find_repeats\n\nr = find_repeats(dna_seq, gap_len, min_len, 0)\nfor rpt in r:\n\t# rpt is a dictionary with keys:\n\t# repeat_number\n\t# first_start\n\t# first_end\n\t# second_start\n\t# second_end\n```\n\nWe are happy to add more output formats, please post a GitHub issue and tag it as an enhancement.\n\n# Installing pydna_repeatfinder\n\nYou should install it using [bioconda](https://bioconda.github.io/):\n\n```\nmamba create -n pydna_repeatfinder -c bioconda pydna_repeatfinder\nmamba activate pydna_repeatfinder\n```\n\n# Citing pydna_repeatfinder\n\nPlease see the citation file.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Frepeatfinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Frepeatfinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Frepeatfinder/lists"}