{"id":22895748,"url":"https://github.com/pseudogene/lava-dna","last_synced_at":"2025-08-12T02:32:20.339Z","repository":{"id":79848616,"uuid":"52591371","full_name":"pseudogene/lava-dna","owner":"pseudogene","description":"LAVA (LAMP Assay Versatile Analysis) is an extendable open-source Loop-mediated  isothermal AMPlification (LAMP)","archived":false,"fork":false,"pushed_at":"2023-08-24T09:35:32.000Z","size":285,"stargazers_count":17,"open_issues_count":2,"forks_count":10,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-07-30T19:59:39.201Z","etag":null,"topics":["bioperl","genetics","lamp","perl-scripts","primer"],"latest_commit_sha":null,"homepage":"","language":"Perl","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/pseudogene.png","metadata":{"files":{"readme":"README","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}},"created_at":"2016-02-26T08:51:57.000Z","updated_at":"2024-06-05T16:50:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"6fde1ce5-122f-4241-8f75-e41407492a2c","html_url":"https://github.com/pseudogene/lava-dna","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/pseudogene%2Flava-dna","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flava-dna/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flava-dna/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flava-dna/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pseudogene","download_url":"https://codeload.github.com/pseudogene/lava-dna/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":["bioperl","genetics","lamp","perl-scripts","primer"],"created_at":"2024-12-13T23:31:50.349Z","updated_at":"2024-12-13T23:31:50.944Z","avatar_url":"https://github.com/pseudogene.png","language":"Perl","readme":"\n[![Build Status](https://travis-ci.org/pseudogene/lava-dna.svg?branch=master)](https://travis-ci.org/pseudogene/lava-dna)\n\nLAVA release 0.1.3\n-------------------\nThis update allows compatibility with the latest primer3 version, in which the thermodynamic parameters have been embedded as part of the code instead of as accessory files.\nAs a result, the thermodynamic path command line argument is no longer needed.\n\n\n\n\nLAVA release 0.1.2 (by Michael Bekaert \u003cmichael.bekaert@stir.ac.uk\u003e)\n------------------\n\nLava has been updated to be compatible with any Linux distribution.\nPart of the source code was updated to allow more parameters to be accesible\nouter_pair_target_length, middle_pair_target_length and inner_pair_target_length.\n\n\n\n\n\nLAVA release 0.1.1 (by Michael Bekaert \u003cmichael.bekaert@stir.ac.uk\u003e)\n------------------\n\nLava has been updated to be compatible with the lasted update of Primer3 and BioPerl.\nPart of the source code was updated to fix syntax errors and deprecated code.\nA new mandatory parameter as been added PRIMER_THERMODYNAMIC_PARAMETERS_PATH, which\nshould provide the path to the primer3_config directory. Usage\n  --thermodynamic_path=path\nor\n  \u003cthermodynamic_path\u003epath\u003c/thermodynamic_path\u003e\n\n\nSYSTEM REQUIREMENTS\n-------------------\n\nPrimer3 2+ (available at http://primer3.sourceforge.net/)\n\tPrimer-selection code\n\nBioPerl 1.6+ (available at http://www.bioperl.org/)\n\tBioPerl's fundamental utilities and file IO are used heavily\n\n\nPRIMER3 REQUIRMENTS\n-------------------\nPRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location. This tag specifies\nthe path to the directory that contains all the parameter files used by the thermodynamic\napproach. In Linux, there are two default locations that are tested if this tag is not\ndefined: ./primer3_config/ and /usr/local/share/primer3/primer3_config/. For Windows,\nthere is only one default location: .\\primer3_config. If the the parameter files are not\nin one these locations, be sure to set PRIMER_THERMODYNAMIC_PARAMETERS_PATH.\n\nSo if you download and compile primer3 form source using the Make command, to get primer3\nto run globally you need to copy the executueable, primer3_core, to your path and place\nthe configuration directory, primer3_config in that same directory or at\n/usr/local/share/primer3/primer3_config/\n\ncd src\nsudo cp primer3_core /usr/local/bin\nsudo mkdir -p /usr/local/share/primer3/\nsudo cp -r primer3_config /usr/local/share/primer3/primer3_config/\n\n\n\n\n\nLAVA release 0.1 (by Clinton Torres \u003cclinton.torres@llnl.gov\u003e)\n----------------\nOriginal distribution and algorithm\n\n\n\nINTRODUCTION\n------------\n\nLAVA (LAMP Assay Versatile Analysis) is an extendable open-source Loop-mediated \nisothermal AMPlification (LAMP).  LAVA identifies combinations of six primer \nregions for basic LAMP signatures, or combinations of eight primer regions for \nLAMP signatures with loop primers, which can be used as LAMP signatures.  The \nidentified primers are conserved among target organism sequences.  Primer \ncombinations are optimized based on lengths, melting temperatures, and spacing \namong primer sites.\n\nThis is a Multiple-Sequence Alignment (MSA) approach to LAMP signature design.  \nEither a single sequence or a pre-computed MSA can be used as input.  The \nindividual sequences from the MSA are used for primer enumeration, with the goal \nof identifying as many locations for primers as possible.  Design parameters can \nbe adjusted for each primer role.  Once primers have been identified that are \nshared among all the individual sequences, they are combined into potential \ninner primer pairs.  Finally, combinations of primers for the remaining roles of \nloop, middle, and outer, are analyzed to select LAMP signature candidates. \n\nThe script slava.pl is also included as a demonstration of scaling to larger\ngenome sizes, but with this kind of implementation, the processing requirements\nscale with the sequence size.  It's realistic to expect that a bacteria-sized\ngenome will take hours to days to execute, depending on the computing resources \navailable.\n\nSYSTEM REQUIREMENTS\n-------------------\n\nThis is a Unix/Linux-only source code release.  It is not unreasonable to assume \nthat the source code can be installed and run on other system types, with a \nminimal amount of effort spent porting, especially since it is primarily \nimplemented in Perl.\n\nPerl library XML::LibXML (available at http://www.cpan.org/)\n\tXML::LibXML is used for some of Options.pm's persistance capabilities\n\nBioPerl 1.5.2 (available at http://www.bioperl.org/)\n\tBioPerl's fundamental utilities and file IO are used heavily\n\t\nPrimer3 1.0 (available at http://primer3.sourceforge.net/)\n\tPrimer-selection code\n\nBio::Perl::Run (also available at http://www.bioperl.org/ as \"bioperl-run\")\n\tBio::Perl::Run::Primer3 is used to execute system-level calls of Primer3\n\n\nINSTALLATION INSTRUCTIONS\n-------------------------\n\nThere are two components to this program, the script lava.pl, and the Perl \nmodules that the script relies on.  Installation of the modules can be \nperformed by entering the top-level directory of the distribution and running:\n\n$ perl Makefile.PL\n$ make\n$ make test\n$ make install\n\nAfter the Perl modules are installed, the script lava.pl can be run from \nanywhere that the installed Perl modules are in the @INC path.\n\n\nACKNOWLEDGEMENTS\n----------------\t\n\nThis work was supported by a NIBIB Point-of-Care Technologies Research Network \nCenter grant (Gerald J. Kost, PI of the UC Davis / LLNL POCT Center, \nNIH U54 EB007959). The content is solely the responsibility of the authors and \ndoes not necessarily represent the official views of the National Institute of \nBiomedical Imaging and Bioengineering or the National Institutes of Health.\n\nThis work performed under the auspices of the U.S. Department of Energy by \nLawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Flava-dna","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpseudogene%2Flava-dna","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Flava-dna/lists"}