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The UCSC SARS-CoV-2 Genome Browser
- Source :
- Nature genetics, vol 52, iss 10, Nature genetics, Nature Genetics
- Publication Year :
- 2020
- Publisher :
- Cold Spring Harbor Laboratory, 2020.
-
Abstract
- BackgroundResearchers 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.ResultsThe UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) 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.ConclusionsWe invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us atgenome-www@soe.ucsc.eduwith 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.
- Subjects :
- Computer science
Protein Data Bank (RCSB PDB)
Rfam
Genome browser
Medical and Health Sciences
Genome
Epitope
0302 clinical medicine
Databases, Genetic
CRISPR
Viral
Lung
0303 health sciences
Phylogenetic tree
Biological Sciences
The Internet
UniProt
Coronavirus Infections
Biotechnology
Pneumonia, Viral
Nucleotide sequencing
Viral Genes
Genome, Viral
Computational biology
Biology
Article
Vaccine Related
Annotation
Databases
Betacoronavirus
03 medical and health sciences
Genetic
Biodefense
Genetics
Humans
Pandemics
030304 developmental biology
Whole genome sequencing
Internet
business.industry
SARS-CoV-2
Prevention
Human Genome
COVID-19
RNA
Pneumonia
Emerging Infectious Diseases
Primer (molecular biology)
business
030217 neurology & neurosurgery
Developmental Biology
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Nature genetics, vol 52, iss 10, Nature genetics, Nature Genetics
- Accession number :
- edsair.doi.dedup.....9e979ac1386e97001df9893d421a1907