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UCSC Genome Browser database

General Information

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

Homepage http://genome.ucsc.edu

Countries that developed this resource United States

Created in 2001

Taxonomic range

Ailuropoda melanoleuca

Alligator Mississippiensis

Balaenoptera acutorostrata scammoni

Bos taurus

Caenorhabditis elegans

Gorilla gorilla gorilla

Heterocephalus glaber

Monodelphis domestica

Mus musculus

Mustela putorius furo

Myotis lucifugus

Nomascus leucogenys

Ochotona princeps

Ornithorhynchus anatinus

Oryctolagus cuniculus

Pongo pygmaeus abelii

Spermophilus tridecemlineatus

Sus scrofa

Takifugu rubripes

Tarsius syrichta

Tetraodon nigroviridis

Trichechus manatus latirostris

Knowledge Domains

Subjects

User-defined Tags

COVID-19

Uniqueness mapping

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: April 17, 2020, 10:05 a.m.; Last accessed: Sep 21 2020 8:54 p.m.

This record is maintained by BrianLee ORCID

Record updated: April 17, 2020, 9:47 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'The FAIRsharing Team' at 09:47, 17 Apr 2020 (approved):

	'onto_disciplines' has been modified:
		Before:
			Comparative Genomics
			Life Science
			Proteomics
			Transcriptomics
		After:
			Comparative Genomics
			Immunology
			Life Science
			Microbiology
			Proteomics
			Transcriptomics
		Added:
			Immunology
			Microbiology
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:49, 16 Apr 2020 (approved):

	'publications' has been modified:
		Before:
			 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
			UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
		After:
			 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
			UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
			The UCSC Genome Browser database: 2019 update|Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2019
			 The UCSC Genome Browser database: 2018 update.|Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. |Nucleic Acids Res.|2018
		Added:
			The UCSC Genome Browser database: 2019 update|Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2019
			 The UCSC Genome Browser database: 2018 update.|Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. |Nucleic Acids Res.|2018
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:46, 16 Apr 2020 (approved):

	'publications' has been modified:
		Before:
			 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
		After:
			 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
			UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
		Added:
			UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:42, 16 Apr 2020 (approved):

	'dataProcesses' has been modified:
		Before:
			daily data releases
			data QA
			versioning by genome assembly
			versioning by individual annotation
			access to historical files possible
			file download(tab-delimited,XML)
			Genome Browser
			Table Browser
			Gene Sorter
			REST API returning JSON data
		After:
			daily data releases
			data QA
			versioning by genome assembly
			versioning by individual annotation
			access to historical files possible
			file download(tab-delimited,XML)
			Genome Browser
			Table Browser
			Gene Sorter
			REST API returning JSON data
			Download Server
			MySQL data server
		Added:
			Download Server
			MySQL data server
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:40, 16 Apr 2020 (approved):

	'dataProcesses' has been modified:
		Before:
			daily data releases
			data QA
			versioning by genome assembly
			versioning by individual annotation
			access to historical files possible
			file download(tab-delimited,XML)
			Genome Browser
			Table Browser
			Gene Sorter
		After:
			daily data releases
			data QA
			versioning by genome assembly
			versioning by individual annotation
			access to historical files possible
			file download(tab-delimited,XML)
			Genome Browser
			Table Browser
			Gene Sorter
			REST API returning JSON data
		Added:
			REST API returning JSON data
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:36, 16 Apr 2020 (approved):

	'tools' has been modified:
		Before:
			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
		After:
			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
			Genome Browser in the Cloud (installation script)||http://genome.ucsc.edu/goldenpath/help/gbic.html
			REST API data interface||http://api.genome.ucsc.edu/
			Gene interactions and pathways from curated databases and text-mining ||http://genome.ucsc.edu/cgi-bin/hgGeneGraph
		Added:
			Genome Browser in the Cloud (installation script)||http://genome.ucsc.edu/goldenpath/help/gbic.html
			REST API data interface||http://api.genome.ucsc.edu/
			Gene interactions and pathways from curated databases and text-mining ||http://genome.ucsc.edu/cgi-bin/hgGeneGraph
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:25, 16 Apr 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
			Uniqueness mapping
		After:
			COVID-19
			Uniqueness mapping
		Added:
			COVID-19
		Removed:

	'miriam_id' has been modified:
		Before: None
		After:

Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'The FAIRsharing Team' at 11:17, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Annotation
			Biological regulation
			Comparative genomics
			DNA microarray
			DNA sequence data
			DNA structural variation To remove
			Deoxyribonucleic acid (DNA)
			Disease phenotype
			Gene
			Gene expression data
			Gene prediction
			Genetic polymorphism
			Genome
			Genotype
			Indel
			Life Science
			Messenger RNA (mRNA)
			Proteomics
			Regulation of gene expression
			Regulatory region
			Ribonucleic acid (RNA)
			Sequence
			Sequence alignment
			Sequence annotation
			Sequence composition, complexity and repeats
			Transcriptomics
			Uniqueness mapping
		After:
			Annotation
			Biological regulation
			Comparative genomics
			DNA microarray
			DNA sequence data
			DNA structural variation
			Deoxyribonucleic acid (DNA)
			Disease phenotype
			Gene
			Gene expression data
			Gene prediction
			Genetic polymorphism
			Genome
			Genotype
			Indel
			Life Science
			Messenger RNA (mRNA)
			Proteomics
			Regulation of gene expression
			Regulatory region
			Ribonucleic acid (RNA)
			Sequence
			Sequence alignment
			Sequence annotation
			Sequence composition, complexity and repeats
			Transcriptomics
			Uniqueness mapping
		Added:
			DNA structural variation
		Removed:
			DNA structural variation To remove

In Collections

Open Science Prize

COVID-19 Resources

RDA Covid-19 WG Resources

Support

General

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
twitter	@GenomeBrowser
wikipedia	https://en.wikipedia.org/wiki/UCSC_Genom ...

Additional Information

Contact

Brian Lee

Tools

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
Genome Browser in the Cloud (installation script)	http://genome.ucsc.edu/goldenpath/help/gbic.html
REST API data interface	http://api.genome.ucsc.edu/
Gene interactions and pathways from curated databases and text-mining	http://genome.ucsc.edu/cgi-bin/hgGeneGraph

Access / Retrieve Data

Conditions of Use

Applies to: General

UCSC Genome Browser Code - License required for commercial use

Data 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
REST API returning JSON data	http://api.genome.ucsc.edu/
Download Server	http://hgdownload.soe.ucsc.edu/downloads.html
MySQL data server	https://genome.ucsc.edu/goldenPath/help/mysql.html

Publications

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