{"id":20153570,"url":"https://github.com/seqan/mars","last_synced_at":"2025-09-14T18:53:09.226Z","repository":{"id":49917346,"uuid":"274127661","full_name":"seqan/mars","owner":"seqan","description":"Motif-based aligned RNA searcher","archived":false,"fork":false,"pushed_at":"2022-08-11T09:59:35.000Z","size":8086,"stargazers_count":0,"open_issues_count":0,"forks_count":2,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-06-09T22:03:33.591Z","etag":null,"topics":["descriptors","motif","rna-structure"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"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/seqan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-06-22T12:13:29.000Z","updated_at":"2021-11-23T17:40:10.000Z","dependencies_parsed_at":"2022-08-29T17:02:36.671Z","dependency_job_id":null,"html_url":"https://github.com/seqan/mars","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":"seqan/app-template","purl":"pkg:github/seqan/mars","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmars","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmars/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmars/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmars/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/mars/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fmars/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275152552,"owners_count":25414450,"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","status":"online","status_checked_at":"2025-09-14T02:00:10.474Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["descriptors","motif","rna-structure"],"created_at":"2024-11-13T23:19:46.115Z","updated_at":"2025-09-14T18:53:09.192Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MaRs: Motif-based aligned RNA searcher\n\n[![Build Status](https://github.com/seqan/mars/workflows/Mars%20CI/badge.svg)](https://github.com/seqan/mars/actions?query=branch%3Amaster+workflow%3A%22Mars%20CI%22)\n[![License](https://img.shields.io/github/license/seqan/mars)](https://github.com/seqan/mars/blob/master/LICENSE.md)\n[![Platforms](https://img.shields.io/badge/platform-Linux%20%7C%20BSD%20%7C%20MacOS-informational.svg)](https://github.com/seqan/mars/blob/master/README.md)\n\nMars is a tool that reads a structural multiple RNA alignment (e.g. from LaRA) and derives fuzzy stem loop descriptors\nfrom it. These descriptors are then subject to a search in a genomic database and Mars returns the hits where the\nRNA structure is found, accompanied with a quality value for each hit.\n\n\n## Download instructions\n\nClone the repository and use the *-\\-recurse-submodules* option for downloading SeqAn as submodule.\n\n```commandline\ngit clone --recurse-submodules https://github.com/seqan/mars.git\n```\n\nAlternatively, you can download a zip package of the repository via the green button at the top of the github page.\nIf you do so, please unzip the file into a new subdirectory named *mars* and download the dependencies separately.\n\n## Requirements\n\n* platforms: Linux, MacOS\n* compiler: gcc ≥ 7\n* cmake ≥ 3.8\n\nMars is dependent on the following libraries:\n\n* [SeqAn 3.0.2](https://github.com/seqan/seqan3.git)\n* [IPknot](http://rtips.dna.bio.keio.ac.jp/ipknot) (shipped in the _lib_ directory) with the following dependencies:\n  * [ViennaRNA 2](https://www.tbi.univie.ac.at/RNA)\n  * [GLPK (GNU Linear Programming Kit) 4](https://www.gnu.org/software/glpk)\n  * [Boost C++ Libraries](https://www.boost.org)\n\n*Note:* Users reported problems with installing ViennaRNA, so we provide some hints here.\n\n1. Install the [GNU MPFR Library](https://www.mpfr.org) first.\n2. Exclude unnecessary components of ViennaRNA:\n   `./configure --without-swig --without-kinfold --without-forester --without-rnalocmin --without-gsl`\n3. If you have linker issues use\n   `./configure --disable-lto`\n4. If your system supports SSE4.1 instructions then we recommend\n   `./configure --enable-sse`\n\nIf you have further suggestions, we are happy to add them here.\n\n## Build instructions\n\nPlease create a new directory and build the program for your platform.\n\n1. create a build directory and visit it: `mkdir build \u0026\u0026 cd build`\n2. run cmake: `cmake ../mars`\n3. build the application: `make`\n4. optional: build and run the tests: `make test`\n5. optional: build the api documentation: `make doc`\n\n## Usage\n\nAfter building the application binary, running Mars is as simple as\n\n```commandline\nbin/mars msa.aln -g genome.fasta\n```\n\nThe resulting genome positions are printed to stdout.\nIf you want to store the result in a file instead, please use the *-o* option or redirect the output.\n\n```commandline\nbin/mars msa.aln -g genome.fasta -o result.txt\nbin/mars msa.aln -g genome.fasta  \u003e result.txt\n```\n\nWe recommend you to specify the number of threads with the *-j* option, in order to enable parallel execution.\nIf you specify *-j 0* the program tries to detect the maximal number of threads available on your machine.\n\n```commandline\nbin/mars msa.aln -g genome.fasta -j 0\n```\n\nFor a list of options, please see the help message:\n\n```commandline\nbin/mars --help\n```\n\n## Authorship \u0026 Copyright\n\nMaRs is being developed by [Jörg Winkler](mailto:j.winkler@fu-berlin.de), but it incorporates a lot of work\nfrom other members of the [SeqAn project](http://www.seqan.de).\n\nYou can ask questions and report bugs on the [GitHub tracker](https://github.com/seqan/mars/issues).\nPlease also [subscribe](https://github.com/seqan/mars/subscription) and/or star us!\nYou can also follow SeqAn on [Twitter](https://twitter.com/SeqAnLib) to receive updates on MaRs.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fmars","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fmars","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fmars/lists"}