{"id":17770316,"url":"https://github.com/timtreis/motivesearch","last_synced_at":"2025-07-31T21:04:30.671Z","repository":{"id":162980670,"uuid":"108995738","full_name":"timtreis/MotiveSearch","owner":"timtreis","description":"A tool to search common motives in promoters after RNASeq analysis ","archived":false,"fork":false,"pushed_at":"2021-03-16T13:14:37.000Z","size":1174,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-07T09:13:37.331Z","etag":null,"topics":["bioinformatics","promoter-analysis"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/timtreis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2017-10-31T12:57:11.000Z","updated_at":"2021-03-16T13:14:40.000Z","dependencies_parsed_at":null,"dependency_job_id":"3c0a67c6-0943-4e36-9a15-dacb4574919d","html_url":"https://github.com/timtreis/MotiveSearch","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/timtreis%2FMotiveSearch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timtreis%2FMotiveSearch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timtreis%2FMotiveSearch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timtreis%2FMotiveSearch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/timtreis","download_url":"https://codeload.github.com/timtreis/MotiveSearch/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246652904,"owners_count":20812213,"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","promoter-analysis"],"created_at":"2024-10-26T21:22:10.765Z","updated_at":"2025-04-01T14:25:12.027Z","avatar_url":"https://github.com/timtreis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MotiveSearch\n\n## Introduction\n\n[under development]\n\n## Workflow\n1. Identify differentially expressed genes. (e.g. RNAseq)\n2. Aquire genomic sequence of host organism and sequences of promoters.\n3. Specify parameters in config.txt. An example is given in the \"Input files\" section.\n4. Determine most frequent kmers in the promoters of the differentially expressed genes.\n5. Determine baseline frequency of those kmers in the entire genome.\n6. Cluster kmers that are found significantly more frequent in the used promoters than in the genome.\n\n\n## Usage\nThe script offers two \n\npython script.py -m PrepareGenome -i genome.fasta\n\npython script.py -m AnalysePromoters -i counttable.txt -t counttable\n## Input files\n\n### config.txt\n```\npath_to_genome = ... // Full path to the genome of the relevant host organism\npath_to_promoters = ... // Full path to the file with the genes promoter sequences\nlist_of_differentially_expressed_genes = ... // file containing a list of gene identifiers\nkmer_length = ... // Length of the kmers that will be searched\ntop_n_kmers = ... // Amount of kmers that should be analysed\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftimtreis%2Fmotivesearch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftimtreis%2Fmotivesearch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftimtreis%2Fmotivesearch/lists"}