{"id":22895752,"url":"https://github.com/pseudogene/uniprime","last_synced_at":"2025-08-12T02:32:22.402Z","repository":{"id":79848623,"uuid":"47559186","full_name":"pseudogene/uniprime","owner":"pseudogene","description":"A workflow-based platform for improved Universal Primer design","archived":false,"fork":false,"pushed_at":"2015-12-08T11:20:22.000Z","size":187,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-07-30T19:59:37.280Z","etag":null,"topics":["bioinformatics","genbank","pcr","primer","taxonomy","universal-primers"],"latest_commit_sha":null,"homepage":"","language":"PHP","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pseudogene.png","metadata":{"files":{"readme":"README","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":"2015-12-07T15:04:23.000Z","updated_at":"2018-05-24T16:40:03.000Z","dependencies_parsed_at":"2023-03-22T01:50:25.991Z","dependency_job_id":null,"html_url":"https://github.com/pseudogene/uniprime","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Funiprime","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Funiprime/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Funiprime/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Funiprime/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pseudogene","download_url":"https://codeload.github.com/pseudogene/uniprime/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229629256,"owners_count":18101263,"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","genbank","pcr","primer","taxonomy","universal-primers"],"created_at":"2024-12-13T23:31:51.935Z","updated_at":"2024-12-13T23:31:52.499Z","avatar_url":"https://github.com/pseudogene.png","language":"PHP","readme":"# $Id: README,v 2.10 2012/09/07 12:35:58 Scotland/Stirling $\n\n                          UniPrime (Ootoowerg) README\n\no INSTALLATION\no TUTORIAL\no COMMAND REFERENCE\no FAQ\n\n\n\no INSTALLATION\n\n  See the INSTALL file.\n\n\n\no TUTORIAL\n\n Here is a simple example of a full execution of UniPrime. Each step can be\n reviewed with the web-companion interface.\n The files you will need uniprime.pm and UniTools.pm are in directory 'bin'\n of the distribution package.\n\n   1. Add a new locus and use the human OAZ1 gene as prototype. The GeneID\n   (4946) is retrieved from GenBank (from the command line in a Terminal\n   window):\n\n     ./uniprime.pl --action=locus --target=4946 -v\n\n   2. Use the locusID provided (e.g. L3.1) and look for orthologues within\n   the class Mammalia and an e-value of 2e-50 as threshold:\n\n     ./uniprime.pl --action=ortho --target=L3.1 -e=2e-50 --query=Mammalia[ORGN] -v\n\n   3. Use the locusID (e.g. L3.1) and establish an alignment and a consensus\n   sequence with a threshold of 60%:\n\n     ./uniprime.pl --action=align --target=L3.1 -c=60 -v\n\n   4. Use the AlignmentID (e.g. A3.2) and design the primer sets:\n\n     ./uniprime.pl --action=primer --target=A3.2 -v\n\n   5. Optionally, use the primer set (e.g. X3.3) and do a virtual PCR with the\n   Mammalian sequence of the WGS databank of the NCBI.\n\n     ./uniprime.pl --action=vpcr --target=X3.3 --db=wgs --query=Mammalia[ORGN] -v\n\no COMMAND REFERENCE\n\n There is only one file controlling UniPrime in bin/uniprime.pl.\n You may find more help by using the command-line help of this file.\n\n     ./uniprime.pl --help\n\n There are five main functions: adding a new locus/gene; searching\n for the orthologous sequences in other species; establishing the\n alignment; designing the primer set and doing a virtual PCR if\n necessary:\n\n     uniprime.pl --action=\u003caction\u003e --target=\u003cID\u003e [options]\n\n  Available actions are:\n   'locus'   Add a new locus:\n    --target GenBank GeneID to be used for this action or fasta file to be used.\n             (mandatory*)\n    --pmid   Associate a reference. (PMID)\n\n   'ortho'   Find new orthologues from mRNA sequences of the locus prototype\n             with BLASTN with the following options:\n    --target LocusID to be used for this action. (mandatory*)\n    --db     Database used when performing the tblastx search. (default\n             value 'refseq_rna')\n    --query  the BLAST search can be limited to the result of an Entrez query\n             against the database chosen. (default none; e.g. 'viruses[ORGN]')\n    --dna    Use DNA rather than mRNA as initial input sequence. (default mRNA)\n    -e       Set the E-value threshold. It is a positive real number. The\n             default is 1e-100. Hit with E-value better than (less than)\n             this threshold will be shown.\n\n   'align'   Provide alignment using T-coffee:\n    --target LocusID to be used for this action. (mandatory*)\n    --dna    Use DNA rather than mRNA as initial input sequence. (default mRNA)\n    -c       Set the threshold to establish the consensus sequence. It is a\n             positive number between 0 and 100. (default 60)\n    --select Specify the sub-set of sequence used for the alignement. (e.g.\n             --select=S3.1 --select=S3.2 --select=S3.4 specify 3 sequences\n             only S3.1, S3.2 and S3.4)\n\n   'primer'  Identify universal primers from consensus sequence:\n    --target AlignmentID to be used for this action. (mandatory*)\n    --size   Optimal size of the amplification. (default 600)\n\n   'vPCR'    Virtual-PCR retrieving all amplicons:\n    --target 'PrimerID to be used for this action. (mandatory*)\n    --db     Database used when performing the tblastx search. (default\n             value 'wgs')\n    --query  the BLAST search can be limited to the result of an Entrez query\n             against the database chosen. (default 'viruses[ORGN]')\n\n   Global options:\n    --aligner either GramAlign or T-coffee. (Default GramAlign)\n    -v       Print verbose output.\n\n\n\no FAQ\n\n Q: Where can I found more help?\n A: UniPrime home page is now https://code.google.com/p/uniprime/\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Funiprime","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpseudogene%2Funiprime","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Funiprime/lists"}