{"id":23505683,"url":"https://github.com/gamcil/5_utr_analysis","last_synced_at":"2025-05-08T22:44:55.410Z","repository":{"id":113168223,"uuid":"232709045","full_name":"gamcil/5_UTR_analysis","owner":"gamcil","description":null,"archived":false,"fork":false,"pushed_at":"2020-01-09T03:57:23.000Z","size":11242,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-07T20:14:41.305Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/gamcil.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":"2020-01-09T02:57:09.000Z","updated_at":"2023-02-10T10:19:13.000Z","dependencies_parsed_at":"2023-03-11T07:30:09.938Z","dependency_job_id":null,"html_url":"https://github.com/gamcil/5_UTR_analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2F5_UTR_analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2F5_UTR_analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2F5_UTR_analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2F5_UTR_analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gamcil","download_url":"https://codeload.github.com/gamcil/5_UTR_analysis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252949281,"owners_count":21830153,"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":"2024-12-25T09:38:59.865Z","updated_at":"2025-05-07T20:14:44.310Z","avatar_url":"https://github.com/gamcil.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 5_UTR_analysis\n\nCode accompanying the paper: \n\n\u003e CRISPRa of biosynthetic gene clusters for bioactive molecule discovery in filamentous fungi\n\u003e\n\u003e Indra Roux, Clara Woodcraft, Jinyu Hu, Rebecca Wolters, Cameron L.M. Gilchrist, Yit-Heng Chooi\n\n## Data\nAll analysis was performed using version 46 of the *A. nidulans* FGSC A4 genome\n obtained from [FungiDB](https://fungidb.org/common/downloads/Current_Release/AnidulansFGSCA4/)\n (FungiDB-46_AnidulansFGSCA4_Genome.fasta and FungiDB-46_AnidulansFGSCA4.gff).\n\n## File summary\n| File | Description |\n| ---- | ----------- |\n| notebook.ipynb | Jupyter notebook containing all code used in analyses |\n| five_prime_UTRs_genome.csv | Summary of 5'UTRs for all genes in *A. nidulans* |\n| five_prime_UTRs_bgcs.csv | Summary of 5'UTRs for genes in *A. nidulans* BGCs |\n| PAM_per_gene_CDS.svg | Total Cas9/Cas12a PAM sites per gene in all genes/genes in BGCs |\n| 5UTR_length_distribution.svg | Distribution of 5'UTR lengths in all genes/genes in BGCs |\n| clusters.csv | Predicted BGCs, adapted from *A. nidulans* [portal on JGI](https://mycocosm.jgi.doe.gov/pages/sm-clusters.jsf?organism=Aspnid1\u0026genomes=Aspnid1\u0026clusterTypes=DMAT%2CHYBRID%2CNRPS%2CNRPS-Like%2CPKS%2CPKS-Like%2CTC\u0026pageSize=50) |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgamcil%2F5_utr_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgamcil%2F5_utr_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgamcil%2F5_utr_analysis/lists"}