{"doi":"10.1101/2020.05.04.075945","title":"The UCSC SARS-CoV-2 Genome Browser","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>\n                    The UCSC Genome Browser for SARS-CoV-2 (\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://genome.ucsc.edu/covid19.html\">https://genome.ucsc.edu/covid19.html</jats:ext-link>\n                    ) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day.\n                  </jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>\n                    We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at\n                    <jats:email>genome-www@soe.ucsc.edu</jats:email>\n                    with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.\n                  </jats:p>\n                </jats:sec>","journal":null,"year":null,"id":634237,"datarank":0.41588830833596724,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.0,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.0,"corpus_percentile":55.5,"corpus_rank":5976,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":20036,"name":"Angie S. Hinrichs","orcid":"0000-0002-1697-1130","position":1,"is_corresponding":false},{"id":109836,"name":"Hiram Clawson","orcid":"0000-0002-0480-0545","position":2,"is_corresponding":false},{"id":109827,"name":"Jairo Navarro Gonzalez","orcid":"0000-0003-4022-4829","position":3,"is_corresponding":false},{"id":1229600,"name":"Brian T. Lee","orcid":"0009-0004-4266-1170","position":4,"is_corresponding":false},{"id":1644805,"name":"Luis R. Nassar","orcid":null,"position":5,"is_corresponding":false},{"id":109830,"name":"Brian J. Raney","orcid":"0000-0002-9708-1390","position":6,"is_corresponding":false},{"id":19975,"name":"Kate R. Rosenbloom","orcid":"0000-0001-8799-4826","position":7,"is_corresponding":false},{"id":58878,"name":"Santrupti Nerli","orcid":"0000-0001-6573-8661","position":8,"is_corresponding":false},{"id":1644807,"name":"Arjun Rao","orcid":null,"position":9,"is_corresponding":false},{"id":109829,"name":"Daniel Schmelter","orcid":"0000-0002-7311-0599","position":10,"is_corresponding":false},{"id":20040,"name":"Ann S. Zweig","orcid":null,"position":11,"is_corresponding":false},{"id":19953,"name":"Todd M. Lowe","orcid":"0000-0003-3253-6021","position":12,"is_corresponding":false},{"id":282092,"name":"Manuel Ares","orcid":"0000-0002-2552-9168","position":13,"is_corresponding":false},{"id":283614,"name":"Russ Corbet-Detig","orcid":null,"position":14,"is_corresponding":false},{"id":282093,"name":"W. James Kent","orcid":"0000-0002-2564-9303","position":15,"is_corresponding":false},{"id":109463,"name":"David Haussler","orcid":"0000-0003-1533-4575","position":16,"is_corresponding":false},{"id":24474,"name":"Maximilian Haeussler","orcid":"0000-0001-8721-8253","position":17,"is_corresponding":false},{"id":109835,"name":"Jason D. Fernandes","orcid":"0000-0002-8625-1796","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The UCSC SARS-CoV-2 Genome Browser","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>\n                    The UCSC Genome Browser for SARS-CoV-2 (\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://genome.ucsc.edu/covid19.html\">https://genome.ucsc.edu/covid19.html</jats:ext-link>\n                    ) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day.\n                  </jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>\n                    We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at\n                    <jats:email>genome-www@soe.ucsc.edu</jats:email>\n                    with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.\n                  </jats:p>\n                </jats:sec>","is_dataset_classified":null,"base_score":2.772588722239781,"endowment":2.772588722239781,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19910364","pmcid":null,"openalex_id":"https://openalex.org/W3023709809","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"1R35GM128932-01","title":"Genetic variation, admixture and genome structure evolution through the lense of Drosophila genomics"},{"funder_name":"National Institutes of Health","grant_id":"1T32CA113275-01A1","title":"Molecular Oncology Training Grant"},{"funder_name":"National Institutes of Health","grant_id":"5U01HG009391-03","title":"Connecting transposable elements and regulatory innovation using ENCODE data"},{"funder_name":"National Institutes of Health","grant_id":"5R01HG007175-02","title":"DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION"},{"funder_name":"National Institutes of Health","grant_id":"5U41HG002371-15","title":"The UCSC Genome Browser"},{"funder_name":"National Institutes of Health","grant_id":"5U41HG010972-02","title":"The WashU-UCSC-EBI Human Genome Reference Center"},{"funder_name":"National Institutes of Health","grant_id":"5U41HG002371-21","title":"The UCSC Genome Browser"},{"funder_name":"National Institutes of Health","grant_id":"5R25DA027995-08","title":"RESEARCH EDUCATION PROGRAM ON COMPUTATIONAL AND STATISTICAL TOOL DEVELOPMENT FOR ADDICTION GENETICS"},{"funder_name":"National Institutes of Health","grant_id":"5U24ES026699-04","title":"THE WASHU TARGET ENVIRONMENTAL EPIGENOMICS DATA COORDINATION CENTER"},{"funder_name":"National Institutes of Health","grant_id":"5U41HG002371-19","title":"The UCSC Genome Browser"}],"total_grants":10,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2020,"count":9},{"year":2021,"count":6}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2020/05/04/2020.05.04.075945.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2020/05/04/2020.05.04.075945.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2020.05.04.075945","host_type":"publisher"},{"url":"https://doi.org/10.1101/2020.05.04.075945","host_type":"repository"},{"url":"https://escholarship.org/uc/item/1506p3q9","host_type":"repository"},{"url":"https://europepmc.org/article/PPR/PPR158722","host_type":"Europe_PMC"},{"url":"https://europepmc.org/api/fulltextRepo?pprId=PPR158722&type=FILE&fileName=EMS93850-pdf.pdf&mimeType=application/pdf","host_type":"Europe_PMC"},{"url":"https://www.nature.com/articles/s41588-020-0700-8.pdf","host_type":""},{"url":"https://doi.org/10.1038/s41588-020-0700-8","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/32908258","host_type":""},{"url":"http://dx.doi.org/10.1038/s41588-020-0700-8","host_type":""},{"url":"https://dx.doi.org/10.1038/s41588-020-0700-8","host_type":""},{"url":"https://dx.doi.org/10.1101/2020.05.04.075945","host_type":""},{"url":"http://dx.doi.org/10.1101/2020.05.04.075945","host_type":""},{"url":"https://doi.org/https://doi.org/10.1038/s41588-020-0700-8","host_type":""}],"fields_of_study":["SARS-CoV-2 and COVID-19 Research","Animal Virus Infections Studies","vaccines and immunoinformatics approaches","0301 basic medicine","03 medical and health sciences"],"mesh_terms":[],"keywords":["Genome browser","Genome","Computational biology","Biology","Ensembl","UniProt","DNA sequencing","Genome project","Genomics","Reference genome","Genetics","Gene","570","Coronaviruses","Agricultural biotechnology","Pneumonia, Viral","Bioinformatics and Computational Biology","610","Genome, Viral","Medical and Health Sciences","Article","Databases","Betacoronavirus","Genetic","Databases, Genetic","Humans","Viral","Pandemics","Internet","SARS-CoV-2","COVID-19","Pneumonia","Biological Sciences","Infectious Diseases","Emerging Infectious Diseases","Coronavirus Infections","Biotechnology","Developmental Biology"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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