EGAEuropean genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.https://ega-archive.org/egabiotools:egaWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0607Laboratory information managementhttp://edamontology.org/topic_3263Data securityhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRD-connectRare DiseaseMatureFree of chargeOpen accessDataSpainhttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/data_2383EGA accession

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

https://ega-archive.org/General10.1038/ng.3312PrimaryEMBL-EBI DatabasesInstituteProviderhelpdesk@ega-archive.orgPersonPrimary contactRosalutionRosalution assists researchers study genetic variation 🧬 in patients 🧑🏾‍🤝‍🧑🏼 by helping select candidate animal models 🐀🐁🐠🪱 to replicate the variation to further research to derive, diagnose, and provide therapies for ultra-rare diseases. Developed by the UAB Center for Computational Genomics and Data Science (CGDS).https://github.com/uab-cgds-worthey/rosalutionrosalutionbiotools:rosalution0.8.8-erWeb applicationhttp://edamontology.org/topic_0199Genetic variationJavaScriptPythonGPL-3.0Rare DiseaseMatureFree of chargehttps://github.com/uab-cgds-worthey/rosalutionRepositoryhttps://github.com/uab-cgds-worthey/rosalution/issuesIssue trackerhttps://github.com/uab-cgds-worthey/rosalution/releases/tag/0.8.8-erSource code0.8.8-er10.21105/joss.05443Angelina Uno-Antonisonhttps://github.com/SeriousHorncatSAMtoolsSAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.http://www.htslib.org/samtoolsbiotools:samtools1.01.11.21.31.3.11.41.4.11.51.61.71.81.91.101.111.121.131.141.151.15.11.161.16.11.171.181.191.19.11.19.21.201.211.21.11.221.22.11.22.21.231.23.1SuiteCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3325Rare diseasesMacLinuxWindowsCMITAnimal and Crop GenomicsRare DiseaseSAMtoolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2573SAM

http://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2573SAM

https://github.com/samtools/samtoolsRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/samtools/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#howtosOtherHowTos for samtoolshttp://www.htslib.org/doc/#manual-pagesUser manualhttp://www.htslib.org/download/Installation instructionshtslibuses10.1093/bioinformatics/btp35219505943PMC2723002PrimaryThe Sequence Alignment/Map format and SAMtools.10.1093/gigascience/giab00833590861PMC7931819PrimaryTwelve years of SAMtools and BCFtools.10.1093/bioinformatics/btr50921903627PMC3198575Richard Durbinrd@sanger.ac.ukPersonContributorWellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportopen-cravatOpenCRAVAT is a new open source, scalable decision support system to support variant and gene prioritization. It offers a dynamic GUI, allowing users to easily, download tools from an extensive resource catalog, create customized pipelines, run jobs at speeds that exceed current variant annotation API services, and explore results in a richly detailed viewing environment. OpenCRAVAT is distinguished from similar tools by the amount and diversity of data resources and computational prediction methods available, which span germline, somatic, common, rare, coding and non-coding variants. We have designed the OpenCRAVAT resource catalog to be open and modular to maximize community and developer involvement, and as a result the catalog is being actively developed and growing larger every month.https://opencravat.orgopen-cravatbiotools:open-cravat2.16.02.17.0Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_3676Exome sequencinghttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAMacLinuxWindowsPythonMITRare DiseaseRare diseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3661SNP annotationhttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCF

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCF

Additional input formats include: list of dbSNP rsIDs, HGVS annotation, and a tab-separated variant annotation format. Output is also in text, excel, and a SQLite database. The SQLIte database format can be loaded into `oc gui` as an interactive web applicationoc run -a ANNOTATOR_LIST input.vcfhttps://run.opencravat.org/ServiceWeb server for running the current version of OpenCRAVAT without needing a local installation.https://github.com/KarchinLab/open-cravatRepositoryhttps://run.opencravat.org/submit/nocache/index.htmlSoftware catalogueCatalogue of modules for OpenCRAVAT, including annotators, variant effect predictors, etc.https://github.com/KarchinLab/open-cravat/releases/Downloads pagehttps://hub.docker.com/r/karchinlab/opencravatContainer filehttps://docs.opencravat.org/en/latest/index.htmlGeneralAPI documentationInstallation instructionsQuick start guideUser manual10.1200/cci.19.0013232228266PMC7113103Kymberleigh A PagelRick KimKyle MoadRachel KarchinBridgeDbBridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.http://bridgedb.github.io/bridgedbbiotools:bridgedb3.0.18Libraryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_2840ToxicologyMacLinuxWindowsJavaApache-2.0ProteomicsELIXIR-NLBIGCAT-UMBridgeDbRare DiseaseMatureFree of chargeInteroperabilityNetherlandshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1025Gene identifier

http://edamontology.org/data_1025Gene identifier

API for converting gene identifiers (Ensembl, Entrez) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifier

http://edamontology.org/data_0989Protein identifier

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1086Compound identifier

http://edamontology.org/data_1086Compound identifier

API for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem, etc) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.https://github.com/bridgedb/BridgeDbRepositoryhttps://github.com/bridgedb/BridgeDb/issuesIssue trackerhttps://fosstodon.org/@bridgedbSocial mediahttps://bridgedb.github.io/pages/docs.htmlGeneralidentifiers.orgusesbioregistryuses10.1186/1471-2105-11-520047655PMC282467810.1007/978-3-319-11964-9_7Primary10.3897/rio.8.e83031PrimaryMaastricht UniversityInstituteProviderWikiPathwaysWikiPathways is a database of biological pathways maintained by and for the scientific community.https://www.wikipathways.org/wikipathwaysbiotools:wikipathwaysWeb APIWeb applicationWeb serviceDatabase portalhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3325Rare diseasesMacLinuxWindowsJavaScriptApache-2.0WikiPathwaysRare DiseaseBIGCAT-UMRD-connectMatureFree of chargeOpen accessNetherlandshttp://edamontology.org/operation_2497Pathway or network analysishttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_0842Identifier

http://edamontology.org/data_0006Datahttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3464JSON

getPathwayhttps://github.com/wikipathways/RepositoryGitHub Organizationhttps://fosstodon.org/@wikipathwaysSocial mediahttps://data.wikipathways.org/Downloads pagehttps://www.wikipathways.org/index.php/WikiPathwaysGeneralhttp://www.wikipathways.org/index.php/Help:WikiPathways_WebserviceAPI documentationbridgedbusesrwikipathwaysusedBy10.1093/nar/gkv102426481357PMC4702772Primary10.1371/journal.pone.000644719649250PMC2714472Primary10.1093/nar/gkaa102433211851PMC777906110.1093/nar/gkx106429136241PMC575327010.1093/nar/gkad96037941138PMC10767877Martina Kutmonmartina.kutmon@maastrichtuniversity.nlhttp://www.wikipathways.org/index.php/WikiPathways:Abouthttps://orcid.org/0000-0002-7699-8191PersonPrimary contactEgon Willighagenhttps://orcid.org/0000-0001-7542-0286PersonAlexander R. Picoapico@gladstone.ucsf.eduPersonPrimary contactrWikiPathwaysUse this package to interface with the WikiPathways API.http://bioconductor.org/packages/release/bioc/html/rWikiPathways.htmlrwikipathwaysbiotools:rwikipathways1.0.01.26.0Libraryhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxRMITRare DiseaseBioConductorCOVID-19Free of chargeMetabolomicsNetherlandshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_3952Pathway ID (WikiPathways)

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3657GPML

https://github.com/wikipathways/rwikipathwaysMirrorhttps://github.com/wikipathways/rwikipathways/issuesIssue trackerhttp://bioconductor.org/packages/release/bioc/src/contrib/rWikiPathways_1.0.0.tar.gzDownloads pagehttp://bioconductor.org/packages/release/bioc/manuals/rWikiPathways/man/rWikiPathways.pdfUser manualbridgedbrusedBywikipathwaysuses10.1093/nar/gkx106429136241PMC5753270Primary10.1093/nar/gkad96037941138PMC10767877Primary10.1093/nar/gkaa102433211851PMC7779061PrimaryEgon Willighagenegon.willighagen@gmail.comhttps://orcid.org/0000-0001-7542-028602jz4aj89PersonPrimary contactAlexander Picoalex.pico@gladstone.ucsf.eduhttps://orcid.org/0000-0001-5706-2163PersonPrimary contactDenise Slenterhttps://orcid.org/0000-0001-8449-131802jz4aj89PersonMartina Kutmonhttps://orcid.org/0000-0002-7699-819102jz4aj89PersonSusan Coorthttps://orcid.org/0000-0003-1224-969002jz4aj89PersonMarvin Martenshttps://orcid.org/0000-0003-2230-084002jz4aj89PersonGENSCANA tool for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.http://hollywood.mit.edu/GENSCAN.htmlmit_splice_predictorbiotools:mit_splice_predictorWeb applicationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0114Gene structurehttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacOtherRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_2454Gene predictionhttp://edamontology.org/operation_0446Exonic splicing enhancer predictionhttp://hollywood.mit.edu/GENSCANinfo.htmlGeneral10.1006/jmbi.1997.09519149143PrimaryChris Burgecburge@mit.eduPersonPrimary contactVISTAComprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.http://genome.lbl.gov/vista/index.shtmlvistabiotools:vistaWeb applicationDatabase portalhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://genome.lbl.gov/vista/help.shtmlGeneral10.1093/bioinformatics/btg4591503387010.1093/nar/gkm27917488840PMC193319210.1093/bioinformatics/btg10051285543710.1093/bioinformatics/16.11.10461115931810.1101/gr.78980312529311PMC43096710.1101/gr.92660312654723PMC43015810.1093/nar/gkh45815215394PMC44159610.1093/nar/gkl82217130149PMC1716724Vista SupportVista@lbl.govPersonPrimary contactAlfredBAM Statistics, Feature Counting and Annotationhttps://github.com/tobiasrausch/alfredalfredbiotools:alfredCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0091BioinformaticsLinuxMacJavaScriptC++BSD-3-ClauseGear GenomicsRare DiseaseEmergingFree of chargeOpen accessToolsEMBLhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0258Sequence alignment analysishttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_2572BAM

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1921Alignment format

https://github.com/tobiasrausch/alfredRepositoryhttps://www.gear-genomics.com/alfred/Servicehttps://www.gear-genomics.com/docs/alfred/User manual10.1093/bioinformatics/bty100730520945PMC6612896PrimaryTobias Rauschtobias.rausch@embl.dehttps://orcid.org/0000-0001-5773-5620PersonDeveloperMaintainerKVFinder-webKVFinder-web is an open-source web-based application of an updated version of parKVFinder software (v1.2.0) for cavity detection and characterization of any type of biomolecular structure, including but not limited to proteins and nucleic acids. KVFinder-web employs a geometric grid-and-sphere-based method with a dual-probe system for efficient cavity detection. The web-based application provides comprehensive characterizations, including shape, volume, area, depth, constitutional, and hydropathy information.https://kvfinder-web.cnpem.br/kvfinder-webbiotools:kvfinder-webv1.1.1Web serviceWeb APIhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0166Protein structural motifs and surfacesMacLinuxWindowsRCOtherApache-2.0COVID-19Rare DiseaseKVFinder suiteMatureFree of chargeOpen accesshttp://edamontology.org/operation_2575Binding site predictionhttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2878Protein structural motifhttp://edamontology.org/format_2330Textual format

https://github.com/LBC-LNBio/KVFinder-webOtherhttps://github.com/LBC-LNBio/KVFinder-web-serviceRepositoryhttps://github.com/LBC-LNBio/KVFinder-web-portalRepositoryhttps://github.com/LBC-LNBio/PyMOL-KVFinder-web-ToolsRepositoryhttps://lbc-lnbio.github.io/KVFinder-web/API documentationparKVFinderusesKVFinderisNewVersionOf10.1093/nar/gkad32437140050PMC10320092Primary10.1021/acs.jcim.3c0032837129917Benchmarking studyJoão V. S. Guerrajoao.guerra@lnbio.cnpem.brhttps://github.com/jvsguerrahttps://orcid.org/0000-0002-6800-4425DeveloperPrimary contactHelder V. Ribeiro-FilhoJosé G. C. PereiraPaulo S. Lopes-de-OliveiraPrimary contactneXtProtneXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.https://www.expasy.org/archives/nextprotnextprotbiotools:nextprotDatabase portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_3120Protein variantshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacCC-BY-4.0Rare DiseaseProteomicsLegacyFree of chargeDataSwitzerlandhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2406Protein structure analysishttps://github.com/calipho-sib/RepositoryneXtProt software repository with issue trackinghttps://twitter.com/nextprot_newsSocial medianeXtProt release news, publications, presentations, tips and more. DM us with feedback!https://www.expasy.org/resources/nextprotSoftware catalogueneXtProt entry in Expasy10.1093/nar/gkz99531724716Primary10.1093/nar/gkr117922139911PMC3245017PrimarySIB Swiss Institute of BioinformaticsInstituteProviderSupportsupport@nextprot.orgPersonPrimary contactPascale Gaudethttp://orcid.org/0000-0003-1813-6857PersonContributorGen SeekerGen Seeker is the browser of variants detected in the Czech population included in the Czech digital genome map. Although Slavs are the largest European ethnolinguistic group, Slavic and especially Czech genomes are underrepresented in international genomic databases, which limits the ability to understand and interpret specific slavic gene variations.https://czechgenome.cz/searchgen_seekerbiotools:gen_seeker1Database portalhttp://edamontology.org/topic_0199Genetic variationMacLinuxWindowsJavaScriptNot licensedELIXIR-CZEATRIS-CZPalacky UniversityRare DiseaseEmergingFree of chargeOpen accessDataHuman Copy Number VariationFederated Human DataRare DiseasesCzech Republichttp://edamontology.org/operation_3918Genome analysishttp://edamontology.org/data_1027Gene ID (NCBI)http://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0860Sequence signature datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3134Gene transcript reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_3134Gene transcript reporthttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3752CSV

https://czechgenome.cz/data-infoGeneralInstitute of Applied Biotechnologies, a.s.InstituteDeveloperPalacky University Olomouc, Czech RepublicInstituteMaintainerMinistry of Industry of the Czech RepublicFunding agencyWikiPathways AppEasy access to pathway content at WikiPathways.org from Cytoscape.http://apps.cytoscape.org/apps/wikipathwayswikipathways_appbiotools:wikipathways_app3.3.1Plug-inhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacShellJavaApache-2.0RD-connectRare DiseaseWikiPathwaysCytoscapeMatureNetherlandshttp://edamontology.org/operation_3439Pathway or network predictionhttp://edamontology.org/operation_0277Pathway or network comparisonhttp://edamontology.org/operation_3562Network simulationhttp://edamontology.org/operation_3083Pathway or network visualisationhttps://github.com/wikipathways/cytoscape-wikipathways-appRepositoryhttps://wikipathways.slack.com/?redir=%2Fmessages%2Fwikipathways-helpdesk%2FHelpdeskhttp://wikipathways.org/index.php/Help:DataVisualizationInCytoscapeTraining material10.12688/F1000RESEARCH.4254.225254103PMC4168754Primary10.1371/journal.pone.000644719649250PMC2714472PrimaryMartina Kutmonmkutmon@gmail.comhttp://orcid.org/0000-0002-7699-8191PersonPrimary contactHomozygosityMapperA web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.http://www.homozygositymapper.orghomozygositymapperbiotools:homozygositymapperWeb applicationhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3500Animalshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseELIXIR-DEMatureFree of chargeGermanyhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3501Over-representation analysishttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_2429Mappinghttp://www.homozygositymapper.org/documentation.htmlGeneral10.1093/nar/gkp36919465395PMC270391510.1093/nar/gks48722669902PMC3394249Supportdominik.seelow@charite.dePersonPrimary contactMutationDistillerMake the analysis of Next-Generation Sequencing data simple. Depending on your background and interest, it offers various modes with optimised settings: Clinical (HPO), Clinical (Gene Panels), Gene Function and Basic Search.https://www.mutationdistiller.org/mutationdistillerbiotools:mutationdistillerWeb applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseELIXIR-DEMatureFree of chargeToolsGermanyhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_3016VCFhttps://www.mutationdistiller.org/MutationDistiller/info/documentation.htmlUser manualhttps://www.mutationdistiller.org/MutationDistiller/info/tutorial.htmlTraining material10.1093/nar/gkz33031106342PMC6602447daniela.hombach@charite.dePersonPrimary contactdominik.seelow@charite.dePersonPrimary contactUMD-PredictorA tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.http://umd-predictor.euumd-predictorbiotools:umd-predictorWeb applicationhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3063Medical informaticsLinuxWindowsMacPHPJavaScriptDeveloped_RD-ConnectRD-ConnectRare DiseaseELIXIR-FRMatureFrancehttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_3197Genetic variation analysis10.1002/humu.2296526842889PMC5067603PrimaryChristophe Beroudchristophe.beroud@univ-amu.frPersonPrimary contactDavid Salgadodavid.salgado@univ-amu.frPersonPrimary contactGeneCardsDatabase of human genes, their products, and involvement in diseases. It automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.http://www.genecards.org/genecardsbiotools:genecardsWeb applicationDatabase portalhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3761Service discoveryhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3436Aggregationhttp://www.genecards.org/GuideGeneral10.1016/s0168-9525(97)01103-79097728Other10.1093/bioinformatics/18.11.154212424129Other10.1093/bioinformatics/14.8.6569789091OtherSupportsupport@lifemapsc.comPersonPrimary contactGenatlasThe Genatlas database provides information on the structure, expression and function of genes, gene mutations and their consequences on diseases.http://www.genatlas.orggenatlasdbbiotools:genatlasdbWeb applicationDatabase portalhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacApache-2.0RD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2495Gene expression analysishttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_3436Aggregation10.1016/s0764-4469(99)80021-39835018Claude Mugnierclaude.mugnier@univ-paris5.frPersonPrimary contactMarie-Liesse Chauvetmarie-liesse.chauvet@inserm.frPersonPrimary contactMartine Lemerrermartine.lemerrer@inserm.frPersonPrimary contactAlexandra Caudealexandra.caude@inserm.frPersonPrimary contactLOVDThe Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.http://www.lovd.nl/3.0/homelovdbiotools:lovd3.0Web applicationDatabase portalhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacPHPGPL-3.0NBICRare DiseaseELIXIR-NLMatureFree of charge (with restrictions)Open accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3197Genetic variation analysishttp://www.lovd.nl/3.0/downloadDownloads pagehttp://www.lovd.nl/3.0/docs/General10.1002/humu.2143821520333PrimaryELIXIR-NLInstituteProviderhttp://www.lovd.nl/3.0/contactPersonPrimary contactMOLGENISA framework for scientific data management, exploration, integration and analysis. It is adaptable to many types of scientific data and data workflows, and there are several pre-configured MOLGENIS systems for specific data types.https://molgenis.orgmolgenisbiotools:molgenis1Web applicationhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRJavaSQLLGPL-3.0NBICRare DiseaseBBMRIBioMedBridges ToolsELIXIR-NLMatureFree of chargeOpen accessInteroperabilityNetherlandshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3436Aggregationhttps://github.com/molgenis/molgenisSource codehttps://molgenis.gitbooks.io/molgenis/content/General10.1093/bioinformatics/btw15527153686PMC4937195Primary10.1186/1471-2105-11-s12-s1221210979PMC3040526UMC Groningen and collaboratorshttp://www.rug.nl/InstituteProviderBioMedBridgeshttp://www.biomedbridges.euConsortiumDocumentorELIXIR-NLhttps://www.dtls.nl/elixir-nl/elixir-nl-2/molgenis-hackers@googlegroups.comPersonPrimary contactMorris Swertzm.a.swertz@rug.nlPersonPrimary contactmolgenis-support@umcg.nlPersonSupportUMDUniversal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones.http://www.umd.be/umdbiotools:umdWeb applicationDatabase portalhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacUnlicenseRD-connectRare DiseaseELIXIR-FRMatureFree of charge (with restrictions)Restricted accessFrancehttp://edamontology.org/operation_3202Polymorphism detectionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0224Query and retrievalhttp://www.umd.be/UMD_Manual.pdfUser manual10.1002/(sici)1098-1004(200001)15:1<86::aid-humu16>3.0.co;2-41061282710.1002/humu.2021016086365Christophe Béroudchristophe.beroud@inserm.frhttp://rd-connect.eu/contacts/christophe-beroud/PersonPrimary contactDavid Salgadodavid.salgado@univ-amu.frRegulationSpotterRegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Phenotypic data can be used to focus on likely disease genes.https://www.regulationspotter.org/RegulationSpotterbiotools:RegulationSpotterWeb applicationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacSQLPerlRare DiseaseRD-connectELIXIR-DEMatureFree of chargeOpen accessGermanyhttp://edamontology.org/operation_3225Variant classification10.1093/nar/gkz32731106382PMC6602480MendelianR-package for heuristic variant filtering.https://github.com/BartBroeckx/Mendelianmendelianbiotools:mendelianCommand-line toolhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRGPL-2.0BIG N2NUGentRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCF

http://edamontology.org/data_3498Sequence variations

http://edamontology.org/data_0916Gene report

https://github.com/BartBroeckx/MendelianGeneral10.1186/s12859-015-0822-726597515PMC4656174Primaryugent.beInstituteProviderBart J. G. BroeckxBart.Broeckx@UGent.behttp://orcid.org/0000-0001-6742-3911PersonPrimary contactFilip Van NieuwerburghFilip.VanNieuwerburgh@UGent.bePersonPrimary contactOrphanetInformation on rare diseases and orphan drugs.http://www.orpha.net/consor/cgi-bin/index.phporphanetbiotools:orphanetWeb applicationDatabase portalhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacDRCATRare DiseaseMatureFree of chargeOpen accessDataFrancehttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2800Orpha number

http://edamontology.org/data_1622Disease reporthttp://edamontology.org/format_2331HTML

http://www.orpha.net/consor/cgi-bin/Education_EducationTools.php?stapage=HM_BLOC_HEADER_HELP_SITEMAP&lng=ENGeneral10.1002/humu.2207822422702PrimaryInserm US14InstituteProviderhttp://www.orpha.net/consor/cgi-bin/Directory_Contact.php?lng=ENPersonPrimary contactESPNHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.http://evs.gs.washington.edu/EVS/espbiotools:espRRID:SCR_012761rridWeb applicationDatabase portalhttp://edamontology.org/topic_3676Exome sequencinghttp://edamontology.org/topic_3408Haematologyhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3322Respiratory medicinehttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3675Variant filteringhttp://edamontology.org/operation_3197Genetic variation analysishttp://evs.gs.washington.edu/EVS/User manual10.1093/hmg/ddt38423962721PMC3782073evsserver@uw.eduPersonPrimary contactMARRVELIntegration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.http://marrvel.org/marrvelbiotools:marrvelRRID:SCR_016871rridDatabase portalhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3077Data acquisitionhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3325Rare diseasesRare Diseasehttp://edamontology.org/operation_2421Database searchhttp://marrvel.org/aboutGeneral10.1016/j.ajhg.2017.04.01028502612PMC5670038Zhandong Liuzhandonl@bcm.eduPersonPrimary contactInterMineOpen source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.http://www.intermine.orginterminebiotools:intermine5.0.0Command-line toolWeb applicationWeb APIDatabase portalhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxMacRRubyJavaPythonJavaScriptPerlLGPL-2.1Rare DiseaseMatureFree of chargeToolsUKhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_2330Textual format

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://github.com/intermine/Source codehttps://repo1.maven.org/maven2/org/intermine/Binarieshttp://intermine.org/im-docsGeneralhttp://intermine.org/intermine-user-docsUser manual10.1093/bioinformatics/bts57723023984PMC3516146Primary10.1093/nar/gku30124753429PMC4086141OtherUniversity of CambridgeInstituteProviderBBSRCFunding agencyContributorWellcome TrustFunding agencyContributorNIHFunding agencyContributorgen.cam.ac.ukInstituteProviderTopHatProgram that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program.http://ccb.jhu.edu/software/tophat/index.shtmltophatbiotools:tophat2.1.1RRID:SCR_013035rridCommand-line toolhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3325Rare diseasesLinuxMacC++galaxyPasteurRare DiseaseTopHatMatureFree of chargeOpen accesshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2749Genome identifierhttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAM

http://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_3003BED

http://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_3003BED

TopHat can find splice junctions without a reference annotation by mapping RNA-Seq reads to a reference genome. The basename of the genome index to be searched. A list of files containing reads. A list of read alignments Track of junctions reported by TopHat. Tracks of insertions and deletions reported by TopHat.https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/tophat_parallel/1.0.0Galaxy servicehttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/tophat/tophat/1.4.1.1Galaxy servicehttp://ccb.jhu.edu/software/tophat/manual.shtmlUser manual10.1093/bioinformatics/btp12019289445PMC2672628Primary10.7490/f1000research.1114334.1OtherDaehwan Kiminfphilo@gmail.comPersonPrimary contactOncoVarAn integrated database and analysis platform for oncogenic driver variants in cancers. OncoVar is a platform to systematically prioritize the oncogenic ability of somatic mutations and cancer genes.https://oncovar.org/oncovarbiotools:oncovarWeb applicationhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3676Exome sequencinghttp://edamontology.org/topic_3325Rare diseasesRare Diseasehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0337Visualisationhttps://oncovar.org/welcome/linksOther10.1093/nar/gkaa103333179738PMC7778899Kun Xiaxiakun@sklmg.edu.cnPersonZhongsheng Sunsunzs@biols.ac.cnPersonFengbiao Maomaofengbiao08@163.comPersonPredictSNP2A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.https://loschmidt.chemi.muni.cz/predictsnp2predictsnp2biotools:predictsnp21.0Web applicationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacJavaScriptJavaProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3019GVFhttp://edamontology.org/format_3016VCF

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3508PDF

VCF file containing scores and PDF file containing scores and database linkshttps://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/Downloads page1.0https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdfUser manual10.1371/journal.pcbi.100496227224906PMC4880439Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportMilos Musilxmusil46@stud.fit.vutbr.czhttps://orcid.org/0000-0001-9373-7930PersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorPredictSNPA consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.https://loschmidt.chemi.muni.cz/predictsnp1predictsnpbiotools:predictsnp1.0Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacJavaScriptJavaPythonProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2291UniProt ID

Prediction of the effect of amino acid substitution on protein functionhttps://loschmidt.chemi.muni.cz/predictsnp1/docs/predictsnp-1.0.tar.gzBinarieshttps://loschmidt.chemi.muni.cz/predictsnp1/docs/USER_GUIDE.pdfUser manualmappusesnssnpanalyzerusespantherusesphd-snpusespolyphenusespolyphen-2usessiftusessnapuses10.1371/journal.pcbi.100344024453961PMC3894168Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportOndrej SalandaPersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderMayo Clinic, Rochester, New York, United States of Americahttps://www.mayoclinic.org/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorPAGEANTPAGEANT (Personal Access to Genome & Analysis of Natural Traits) is a self-completion genetic reporting tool for DTC genetic testers.https://github.com/jielab/pageantpageantbiotools:pageantDesktop applicationhttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/topic_3298Phenomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_0102MappingMacLinuxWindowsPythonRare Diseasehttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3891Essential dynamicshttps://github.com/jielab/pageant/issuesIssue tracker10.1093/nar/gkab124534928375PMC9023285Primaryvalerio.napolioni@unicam.itvalerio.napolioni@unicam.itPersonPrimary contactJie Huangjiehuang001@pku.edu.cnPersonPrimary contactWaveQTLWavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assayshttps://github.com/heejungshim/WaveQTLwaveqtlbiotools:waveqtlCommand-line toolhttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0102MappingLinuxRC++GPL-3.0Animal and Crop GenomicsRare Diseasehttp://edamontology.org/operation_0282Genetic mappinghttps://github.com/heejungshim/WaveQTLGeneral10.1214/14-aoas77629399242PMC579562110.1186/s12864-021-07582-633932983PMC8088671https://groups.google.com/forum/?hl=en#!forum/waveqtlusersPersonPrimary contactBridgeDbRUse BridgeDb functions and load identifier mapping databases in R.http://bioconductor.org/packages/release/bioc/html/BridgeDbR.htmlbridgedbrbiotools:bridgedbr1.8.02.4.0Command-line toolLibraryhttp://edamontology.org/topic_3345Data identity and mappinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRGPL-3.0Rare DiseaseBridgeDbBioConductorMatureOpen accessInteroperabilityNetherlandshttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/data_1025Gene identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2108Reaction IDhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0989Protein identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1086Compound identifierhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1025Gene identifierhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2108Reaction IDhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0989Protein identifierhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1086Compound identifierhttp://edamontology.org/format_2330Textual format

https://github.com/bridgedb/BridgeDbMirrorhttps://github.com/BiGCAT-UM/bridgedb-rMirrorhttp://bioconductor/packages/release/bioc/src/contrib/BridgeDbR_1.8.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/BridgeDbR.htmlUser manual10.1186/s12859-015-0708-826298294PMC4546821ReviewEgon Willighagenegon.willighagen@gmail.comPersonPrimary contactStrVCTVREMethod that predicts the pathogenicity of deletions and duplications that affect one or more exons.https://strvctvre.berkeley.edu/strvctvrebiotools:strvctvreWeb applicationCommand-line toolhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_3958Copy number variationhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_0622GenomicsLinuxPythonMITRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3003BEDhttps://github.com/andrewSharo/StrVCTVRERepositoryhttps://github.com/andrewSharo/StrVCTVRESource codehttps://strvctvre.berkeley.edu/General10.1016/j.ajhg.2021.12.00735032432PMC8874149Andrew Sharosharo@compbio.berkeley.eduhttps://andrewsharo.com/CADDCombined Annotation Dependent Depletion (CADD) - tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.http://cadd.gs.washington.edu/cadd_phredbiotools:cadd_phredWeb applicationhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacUnlicenseRD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_2238Statistical calculationhttps://cadd.gs.washington.edu/downloadDownloads pagehttp://cadd.gs.washington.edu/infoGeneral10.1038/ng.289224487276PMC3992975Primary10.1093/nar/gky101630371827PMC632389210.1186/s13073-021-00835-933618777PMC7901104CADD supportcadd-support@uw.eduPersonPrimary contactUCSC Genome BrowserLarge database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users own annotation data.https://genome.ucsc.edu/ucsc_genome_browserbiotools:ucsc_genome_browserWeb applicationDatabase portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacApache-2.0Rare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0308PCR primer designhttps://genome.ucsc.edu/goldenPath/help/hgTracksHelp.htmlGeneral10.1093/nar/gkp93919906737PMC280887010.1093/nar/gkr101222075998PMC324518310.1093/nar/gkr105522086951PMC324501810.1101/gr.22910212045153PMC186604Primary10.1093/nar/gkg12912519945PMC16557610.1093/nar/gkm96618086701PMC223883510.1093/nar/gkj14416381938PMC134750610.1093/nar/gkn87518996895PMC268646310.1093/nar/gkt116824270787PMC396494710.1093/nar/gku117725428374PMC438397110.1093/nar/gkv127526590259PMC470290210.1093/nar/gkw113427899642PMC521059110.1093/nar/gky109530407534PMC632395310.1093/nar/gks104823155063PMC353108210.1093/nar/gkq96320959295PMC3242726Brooke Rheadrhead@soe.ucsc.eduhttps://genome.ucsc.edu/contacts.htmlPersonPrimary contactOMIMOnline Mendelian inheritance in Man (OMIM) - catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIMomimbiotools:omimWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacUnlicenseRD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_3763Service invocationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3197Genetic variation analysishttp://omim.org/General10.1093/nar/gki03315608251PMC539987Primary10.1093/nar/gku120525428349PMC438398510.1093/nar/gky115130445645PMC632393710.1093/nar/gkn66518842627PMC2686440Ada Hamoshahamosh@jhmi.eduPersonPrimary contactGWAS catalogA catalogue that provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5.https://www.ebi.ac.uk/gwas/gwas_catalogbiotools:gwas_catalogWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacApache-2.0RD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_3459Functional clusteringhttp://edamontology.org/operation_2429Mappinghttps://www.ebi.ac.uk/gwas/downloadsDownloads pagehttps://www.ebi.ac.uk/gwas/docsGeneralhttps://github.com/EBISPOT/gociGeneral10.1093/nar/gkt122924316577PMC396511910.1093/nar/gkw113327899670PMC521059010.1093/nar/gky112030445434PMC6323933PrimaryGWAS Catalog Supportgwas-info@ebi.ac.ukPersonPrimary contactANNOVARA tool for finding relevant genetic variants from high-throughput sequencing data based on functional annotation.http://annovar.openbioinformatics.org/en/latest/annovarbiotools:annovarCommand-line toolWeb servicehttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacPerlRare DiseaseANNOVARMatureFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_3672Gene functional annotationhttp://annovar.openbioinformatics.org/en/latest/General10.1093/nar/gkq60320601685PMC2938201Primary10.1038/nprot.2015.10526379229PMC471873410.1136/jmedgenet-2012-10091822717648PMC3556337Kai Wangkai@openbioinformatics.orgPersonPrimary contactReMM scoreReMM score is a tool that scores the positions in the human genome in terms of their regulatory probability. We use curated regulatory variants involved in Mendelian disease and contrast them with proxy-neutral variants that survived natural selection in a machine learning framework. We use an algorithm for highly imbalanced data, called hyperSMURF, to differentiate deleterious from neutral variants.https://remm.bihealth.org/remm_scorebiotools:remm_scorev0.3.1.post1v0.4Web applicationWorkflowWeb APIBioinformatics portalhttp://edamontology.org/topic_3173Epigenomicshttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0085Functional genomicsLinuxMITRare DiseaseOpen accesshttps://github.com/kircherlab/ReMMRepositoryhttps://doi.org/10.5281/zenodo.6576087Downloads pagev0.4https://remm.bihealth.org/General10.1016/j.ajhg.2016.07.00527569544PMC5011059Primary10.1101/2022.03.14.484240Max Schubachmax.schubach@bih-charite.dehttps://orcid.org/0000-0002-2032-6679Martin Kirchermartin.kircher@bih-charite.dehttps://orcid.org/0000-0001-9278-5471Lusiné Nazaretyanlusine.nazaretyan@bih-charite.dehttps://orcid.org/0000-0001-5820-4143RD-Connect Genome-Phenome Analysis Platform (GPAP)An online tool for diagnosis and gene discovery in rare disease research. The platform features allow identifying disease-causing mutations in rare disease patients and linking them with detailed clinical information.https://platform.rd-connect.eu/rd-connect_platformbiotools:rd-connect_platformWeb applicationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3473Data miningLinuxWindowsMacRD-connectRare DiseaseELIXIR-ESINBRIS3CAT VEISEmergingFree of charge (with restrictions)Restricted accessSpainhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_0361Sequence annotation10.1002/humu.2435335178824PMC9324157Primary10.1007/s11606-014-2908-825029978PMC4124112OtherSteven Lauriesteven.laurie@cnag.crg.euPersonPrimary contactDavide Pisciadavide.piscia@cnag.crg.euPersonContributorLeslie Matalongaleslie.matalonga@cnag.crg.euPersonContributorAlberto Corvóalberto.corvo@cnag.crg.euPersonContributorMarcos Fernández-Callejomarcos.fernandez@cnag.crg.euPersonContributorCarles Garcia-Linarescarles.garcia@cnag.crg.euPersonContributorCarles Hernandez-Ferrercarles.hernandez@cnag.crg.euhttp://www.carleshf.comhttps://orcid.org/0000-0002-8029-7160PersonContributorCristina LuengoPersonContributorInés MartínezPersonContributorAnastasios Papakonstantinouanastasios.papakonstantinou@cnag.crg.euPersonContributorDaniel Picó-Amadordaniel.pico@cnag.crg.euPersonContributorJoan ProtasioPersonContributorRachel ThompsonPersonSupportRaul Tondaraul.tonda@cnag.crg.euPersonContributorMònica BayésPersonContributorGemma Bullichgemma.bullich@cnag.crg.euPersonContributorJordi Camps-PuchadasPersonContributorIda Paramonovida.paramonov@cnag.crg.euPersonContributorJean-Rémi Trottajeanremi.trotta@cnag.crg.euPersonContributorAngel AlonsoMarcella AttimonelliPersonSupportChristophe BéroudPersonSupportVirginie Bros-FacerPersonSupportOrion J. BuskePersonSupportAndrés Cañada-PallarésPersonSupportJosé M. FernándezPersonSupportMats G. HanssonPersonSupportRita HorvathPersonSupportJulius O.B. JacobsenPersonSupportRajaram KaliyaperumalPersonSupportSéverine Lair-PréterrePersonSupportLuana LicataPersonSupportPedro LopesPersonSupportEstrella López-MartínPersonSupportDeborah MascalzoniPersonSupportLucia MonacoPersonSupportLuis A. Pérez-JuradoPersonSupportManuel Posada de la PazPersonSupportJordi RamblaPersonSupportAna RathPersonSupportOlaf RiessPersonSupportPeter N. RobinsonPersonSupportDavid SalgadoPersonSupportDamian SmedleyPersonSupportDylan SpaldingPersonSupportPeter A. C. 't HoenPersonSupportAna TöpfPersonSupportIrina ZaharievaPersonSupportHolm GraessnerPersonSupportIvo G. Gutivo.gut@cnag.crg.euPersonSupportHanns Lochmüllerhlochmuller@toh.caPersonSupportSergi Beltransergi.beltran@cnag.crg.euPersonPrimary contactRVSDetection of rare disease variants in extended pedigrees using RVS. Computes estimates of the probability of related individuals sharing a rare variant. Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test). ExomeSeq, Genetics, GenomeWideAssociation, ImmunoOncology, Software, VariantDetection, WholeGenome.https://bioconductor.org/packages/release/bioc/html/RVS.htmlrvs_softwarebiotools:rvs_softwareLibraryhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseasesRGPL-2.0Rare Diseasehttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3791Collapsing methods10.1093/bioinformatics/bty97630500888PMC6612888Ingo Ruczinskiingo@jhu.eduPersonVariant Combination Pathogenicity Predictor (VarCoPP) 2.0VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. A variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). VarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. VarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel. You can use it through the online tool ORVAL: https://orval.ibsquare.be.http://varcopp.ibsquare.beVariant_Combinaton_Pathogenicity_Predictorbiotools:Variant_Combinaton_Pathogenicity_Predictor1.02.0Plug-inhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0625Genotype and phenotypeLinuxWindowsMacGPL-3.0ELIXIR-BERD-ConnectRare DiseaseMatureFree of chargeOpen accessRare DiseasesBelgiumhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_3197Genetic variation analysishttps://github.com/oligogenic/VarCoPP2.0Repositoryhttps://github.com/sofiapapad90/VarCoPP/Repositoryhttps://orval.ibsquare.beServiceWeb app integrating VarCoPP2.0oligogenic_resource_for_variant_analysisincludedInolidauses10.1073/pnas.181560111631127050PMC65756321.010.1186/s12859-023-05291-337127601PMC101527952.0Tom Lenaertstlenaert@ulb.ac.behttp://www.ibsquare.behttps://orcid.org/0000-0003-3645-1455PersonPrimary contactSofia Papadomitriousofiapapad.bio@gmail.comPersonDeveloperInteruniversity Institute of Bioinformatics in Brusselshttps://ibsquare.beInstituteProviderDigenic Diseases Database (DIDA)Digenic Diseases Database (DiDA) provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.http://dida.ibsquare.bedidabiotools:didaWeb applicationDatabase portalhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacCC-BY-NC-4.0ELIXIR-BERD-ConnectRare DiseaseLegacyFree of chargeOpen accessRare DiseasesBelgiumhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3661SNP annotationhttp://edamontology.org/operation_3197Genetic variation analysishttp://dida.ibsquare.be/help/Generalhttp://dida.ibsquare.be/documentation/GeneralMore detailed documentation.olidahasNewVersion10.1093/nar/gkv106826481352PMC4702791PrimaryInteruniversity Institute of Bioinformatics in Brusselshttps://www.ibsquare.beInstituteProviderTom Lenaertstlenaert@ulb.ac.behttp://www.ibsquare.behttps://orcid.org/0000-0003-3645-1455PersonPrimary contactCharlotte NachtegaelCharlotte.Nachtegael@ulb.ac.bePersonMaintainerOligogenic resource for variant analysis (ORVAL)ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques.https://orval.ibsquare.beOligogenic_resource_for_variant_analysisbiotools:Oligogenic_resource_for_variant_analysis3.0.0Web servicehttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_1775Function analysishttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacCC-BY-4.0ELIXIR-BERD-connectRare DiseaseMatureFree of chargeOpen accessRare DiseasesBelgiumhttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_3439Pathway or network predictionhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttps://orval.ibsquare.be/documentationUser manualFAQhttps://orval-dev.ibsquare.be/updatesRelease notesvariant_combinaton_pathogenicity_predictoruses10.1093/nar/gkz43731147699PMC6602484Tom Lenaertstlenaert@ulb.ac.behttps://www.ibsquare.behttps://orcid.org/0000-0003-3645-1455PersonPrimary contactAlexandre Renauxalexandre.renaux@ulb.ac.behttps://www.ibsquare.bePersonDeveloperInteruniversity Institute of Bioinformatics in Brusselshttps://www.ibsquare.beInstituteProviderHGMDThe Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications including searching for an overview of known mutations associated with a particular disease, interpreting clinical test results or looking for the likely causal mutation in a list of variants.http://www.hgmd.orghgmdbiotools:hgmdRRID:SCR_001621rridWeb applicationDatabase portalhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2815Human biologyhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRD-connectRare DiseaseMatureFree of charge (with restrictions)Restricted accesshttp://edamontology.org/operation_3224Gene set testinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3197Genetic variation analysishttp://www.hgmd.cf.ac.uk/docs/new_help.htmlGeneral10.1007/s00439-013-1358-424077912PMC3898141Primary10.1136/jmg.2007.0552101824539310.1002/humu.102121275470210.1186/gm1319348700PMC265158610.1007/s00439-017-1779-628349240PMC5429360Contact Formhttp://www.hgmd.cf.ac.uk/docs/comment_form.htmlPersonPrimary contactCytoscapeOpen source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.http://www.cytoscape.org/cytoscapebiotools:cytoscape3.7.1Suitehttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRare DiseaseEBI Training ToolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3562Network simulationhttp://edamontology.org/operation_3083Pathway or network visualisationhttps://cytoscape.org/download.htmlDownloads pagehttps://github.com/cytoscape/cytoscape-tutorials/wikiTraining materialTutorial materialhttps://github.com/cytoscape/cytoscapeGeneralscnetvizuses10.1101/gr.123930314597658PMC403769https://groups.google.com/forum/?fromgroups#!forum/cytoscape-helpdeskPersonPrimary contactWS-SNPs-and-GOA web server for predicting disease associated variations from protein sequence and structure.http://snps.biofold.org/snps-and-gows_snps_and_gobiotools:ws_snps_and_go2.0Web applicationWeb servicehttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacRare DiseaseMatureFree of chargeOpen accessRare DiseasesItalyhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1467Protein chainhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1176GO concept IDhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2209Mutation IDhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1622Disease reporthttp://edamontology.org/format_2331HTML

SNPs&GO 3Dhttps://hub.docker.com/r/biofold/snps-and-goContainer file2.0http://snps.biofold.org/snps-and-go/General10.1186/1471-2105-12-s4-s321992054PMC3194195Method10.1002/humu.2104719514061PrimaryELIXIR-ITA-BOLOGNAhttp://www.biocomp.unibo.itInstituteProviderEmidio Capriottiemidio.capriotti@gmail.comhttp://orcid.org/0000-0002-2323-0963PersonDeveloperPrimary contactRita Casadiocasadio@biocomp.unibo.itPersonPrimary contact