{"id":18256431,"url":"https://github.com/baderlab/powclui","last_synced_at":"2025-04-08T22:27:35.102Z","repository":{"id":146738772,"uuid":"156309909","full_name":"BaderLab/POWCLUI","owner":"BaderLab","description":"POW! PDZ domain-peptide interaction prediction command line user interface","archived":false,"fork":false,"pushed_at":"2018-11-06T02:00:51.000Z","size":15433,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-02-14T17:42:38.416Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BaderLab.png","metadata":{"files":{"readme":"Readme.txt","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":"2018-11-06T01:49:16.000Z","updated_at":"2018-11-15T01:39:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"2687b21c-07b7-452b-a3b2-6c4e01fcd9e6","html_url":"https://github.com/BaderLab/POWCLUI","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/BaderLab%2FPOWCLUI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaderLab%2FPOWCLUI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaderLab%2FPOWCLUI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaderLab%2FPOWCLUI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BaderLab","download_url":"https://codeload.github.com/BaderLab/POWCLUI/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247937436,"owners_count":21021257,"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":"2024-11-05T10:21:53.522Z","updated_at":"2025-04-08T22:27:35.085Z","avatar_url":"https://github.com/BaderLab.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"README\n======\nPOWSeqCLUI (POW Seq Command Line User Interface)\nPOWStructCLUI (POW Struct Command Line User Interface)\n\nApril 10, 2013\nAuthors: Shirley Hui, Gary D. Bader\nUniversity of Toronto, Dept. Molecular Genetics\n\nPlease cite:\nHui S, Bader GD, BMC Bioinformatics 2010, 11:507\nHui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27\n\nSoftware is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007\n\nWebsite version: http://webservice.baderlab.org/domains/POW/\n\nREQUIREMENTS\n============\nThis software is a java application and is confirmed to run under Java version 1.5.0_30.\n\nHOW TO RUN\n==========\n\n1) Unzip POWCLUI.zip in a directory\n2) At the command line, run one of the following commands in the directory above.\n\nPOWSeqCLUI:\njava -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWSeqCLUI \u003corganism\u003e \u003cdomain name file\u003e \u003cpeptide file\u003e\n\nPOWStructCLUI:\njava -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWStructCLUI \u003corganism\u003e \u003cdomain name file\u003e \u003cpeptide file\u003e\n\nParameters:\n\u003corganism\u003e: H = Human, M = Mouse, W = Worm, F = Fly\n\u003cdomain name file\u003e: Path to a file containing the PDZ domain names (one per line)\n\u003cpeptide file\u003e: Path to a file containing the peptides of length five (one per line)\n\nNote: POWCLUI takes exactly three parameters.\n\nOUTPUT\n======\nDomain names that are repeated or not supported are skipped.\nPeptides that are too short (\u003c 5), contain invalid residues or are repeated are skipped.\nPeptides that are too long (\u003e 5) are truncated and skipped if repeated.\nThe programs will output information for all predictions (positive and negative).\n\nInformation reported include:\n* Domain Name\n* Binding Site Sequence (POWSeqCLUI only)\n* Peptide Sequence\n* Decision Value\n\nEXAMPLES\n========\n1) POWSeqCLUI Output:\n\n\u003ejava -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWSeqCLUI H examples/PDZDomains.txt examples/Peptides.txt\nPOWSeqCLUI (POW Seq Command Line User Interface)\nApril 10, 2013\nAuthors: Shirley Hui, Gary D. Bader\nUniversity of Toronto, Dept. Molecular Genetics\n\nPlease cite:\nHui S, Bader GD, BMC Bioinformatics 2010, 11:507\nHui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27\n\nSoftware is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007\n\nOrganism: H\nDomain Names:\n\tError: Domain BLAH not supported, skipping...\n\t2 domain(s) read...\nPeptides:\n\tWarning: Peptide EDTWV already in list, skipping...\n\tError: Peptide S too short, skipping...\n\tWarning: Peptide SSEDTWV too long, truncating...\n\tWarning: Peptide EDTWV already in list, skipping...\n\tError: Invalid residue in peptide 12345, skipping...\n\t3 peptide(s) read...\nResults: \nDomainName\tBindingSiteSequence\tPeptideSequence\tDecisionScore\nDLG1-1\tGLGFSIAGTKIGHSVA\tFLGWF\t-1.8040996291275562\nDLG1-1\tGLGFSIAGTKIGHSVA\tEDTWV\t-0.19450785721099295\nDLG1-1\tGLGFSIAGTKIGHSVA\tSSSSS\t-1.3645443983035186\nMPDZ-1\tSLGFSVVGQEQSHQIA\tFLGWF\t0.6199364236346863\nMPDZ-1\tSLGFSVVGQEQSHQIA\tEDTWV\t0.5265758575783792\nMPDZ-1\tSLGFSVVGQEQSHQIA\tSSSSS\t-1.3837781314980506\n\n1) POWStructCLUI Output:\n\n\u003ejava -cp .:lib/libsvm-2.89-pdzsvm.jar org.baderlab.pdzsvm.analysis.POWStructCLUI H examples/PDZDomains.txt examples/Peptides.txt \nPOWStructCLUI (POW Struct Command Line User Interface)\nApril 10, 2013\nAuthors: Shirley Hui, Gary D. Bader\nUniversity of Toronto, Dept. Molecular Genetics\n\nPlease cite:\nHui S, Bader GD, BMC Bioinformatics 2010, 11:507\nHui S, Xing X, Bader GD, BMC Bioinformatics 2013, 14:27\n\nSoftware is distribued AS IS under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007\n\nOrganism: H\nDomain Names:\n\tError: Domain BLAH not supported, skipping...\n\t2 domain(s) read...\nPeptides:\n\tWarning: Peptide EDTWV already in list, skipping...\n\tError: Peptide S too short, skipping...\n\tWarning: Peptide SSEDTWV too long, truncating...\n\tWarning: Peptide EDTWV already in list, skipping...\n\tError: Invalid residue in peptide 12345, skipping...\n\t3 peptide(s) read...\nResults: \nDomainName\tPeptideSequence\tDecisionScore\nMPDZ-1\tFLGWF\t1.3722791766167184\nMPDZ-1\tSSSSS\t-2.298175924389645\nMPDZ-1\tEDTWV\t0.6017692863722264\nDLG1-1\tFLGWF\t-1.214349274364786\nDLG1-1\tSSSSS\t-2.5483924802411475\nDLG1-1\tEDTWV\t0.9241258336582265\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaderlab%2Fpowclui","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbaderlab%2Fpowclui","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaderlab%2Fpowclui/lists"}