UCSC Genome Browser database
Homepage http://genome.ucsc.edu
Developed in United States
Created in 2001
Taxonomic range
Knowledge Domains BETA
Subjects BETA
User-defined Tags
How to cite this record FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 23 2019 10:13 a.m.
Record updated: Nov. 21, 2018, 11:17 a.m. by The FAIRsharing Team.
| FAQ | http://genome.ucsc.edu/FAQ/ |
| contact form | http://genome.ucsc.edu/cgi-bin/hgUserSug ... |
| support email | genome@soe.ucsc.edu |
| forum | https://groups.google.com/a/soe.ucsc.edu ... |
| help | http://genome.ucsc.edu/goldenPath/help/h ... |
| training | http://genome.ucsc.edu/training.html |
| @GenomeBrowser | |
| wikipedia | https://en.wikipedia.org/wiki/UCSC_Genom ... |
Additional Information
| Contact | Brian Lee |
| Blat | http://genome.ucsc.edu/cgi-bin/hgBlat |
| In Silico PCR | http://genome.ucsc.edu/cgi-bin/hgPcr |
| Genome Graphs | http://genome.ucsc.edu/cgi-bin/hgGenome |
| VisiGene | http://genome.ucsc.edu/cgi-bin/hgVisiGene |
| liftOver | http://genome.ucsc.edu/cgi-bin/hgLiftOver |
| Variant Annotation Integrator (VAI) | http://genome.ucsc.edu/cgi-bin/hgVai |
| Data Integrator | http://genome.ucsc.edu/cgi-bin/hgIntegrator |
| Genome Browser in a Box (virtual machine) | http://genome.ucsc.edu/goldenpath/help/gbib.html |
Conditions of Use
Applies to: GeneralData Versioning
| versioning by genome assembly | No link recorded |
| versioning by individual annotation | No link recorded |
| access to historical files possible | No link recorded |
Data Release
| daily data releases | No link recorded |
Data Curation
| data QA | No link recorded |
Data Access
| file download(tab-delimited,XML) | No link recorded |
| Genome Browser | http://genome.ucsc.edu/ |
| Table Browser | http://genome.ucsc.edu/cgi-bin/hgTables |
| Gene Sorter | http://genome.ucsc.edu/cgi-bin/hgNear |
The UCSC Genome Browser database: extensions and updates 2013
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.
Nucleic Acids Res 2013
The UCSC Table Browser data retrieval tool
Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ.,
Nucleic Acids Res. 2004
The human genome browser at UCSC
Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D.,
Genome Res. 2002
ENCODE data in the UCSC Genome Browser: year 5 update
Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ
Nucleic Acids Res. 2013
BLAT--the BLAST-like alignment tool.
Kent WJ.,
Genome Res. 2002
Exploring relationships and mining data with the UCSC Gene Sorter
Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D
Genome Res. 2005
The UCSC Genome Browser
Karolchik D, Hinrichs AS, Kent WJ
Curr Protoc Bioinformatics 2012
Initial sequencing and analysis of the human genome
Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.
Nature 2001
Assembly of the working draft of the human genome with GigAssembler.
Kent WJ., Haussler D.,
Genome Res. 2001
The UCSC Genome Browser database: 2016 update.
Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ
Nucleic Acids Res 2015
The UCSC Genome Browser database: 2015 update.
Rosenbloom KR,Armstrong J,Barber GP,Casper J,Clawson H,Diekhans M,Dreszer TR,Fujita PA,Guruvadoo L,Haeussler M,Harte RA,Heitner S,Hickey G,Hinrichs AS,Hubley R,Karolchik D,Learned K,Lee BT,Li CH,Miga KH,Nguyen N,Paten B,Raney BJ,Smit AF,Speir ML,Zweig AS,Haussler D,Kuhn RM,Kent WJ
Nucleic Acids Res 2014
The UCSC Genome Browser database: 2017 update.
Tyner C,Barber GP,Casper J,Clawson H,Diekhans M,Eisenhart C,Fischer CM,Gibson D,Gonzalez JN,Guruvadoo L,Haeussler M,Heitner S,Hinrichs AS,Karolchik D,Lee BT,Lee CM,Nejad P,Raney BJ,Rosenbloom KR,Speir ML,Villarreal C,Vivian J,Zweig AS,Haussler D,Kuhn RM,Kent WJ
Nucleic Acids Res 2016
Reporting Guidelines
No guidelines defined
Terminology Artifacts
No semantic standards defined
Models and Formats
- Axt Alignment Format
- Binary sequence information Format
- Chain Format for pairwise alignment
- Big Browser Extensible Data Format
- bigWig Track Format
- microarray track data Browser Extensible Data Format
- Personal Genome SNP Format
- Multiple Alignment Format
- Gene Transfer Format
- Gene Feature File version 1
- BLAST-like Alignment Tool Format
- Browser Extensible Data Format
- nucleotide inFormation binary Format
- Binary Alignment Map Format
- Variant Call Format
- Wiggle Track Format
- Big Multiple Alignment Format
- Big Pattern Space Layout
- net alignment annotation Format
- Gene Prediction File Format
- Big Gene Prediction
- Big Chain
Metrics
No metrics standards defined
This record is not implemented by any policy.
Record Maintainer
This record is maintained by dkarolchik and BrianLee ORCID
Funds
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
Maintains
