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The UCSC Genome Browser

The UCSC Genome Browser

The web application provides a radpid display of chosen section of genome sequences and tens of aligned annotation annotation tracks, such as ESTs, mRNAs, CpG islands, known genes, predicted genes, assembly gaps, assembly coverage, chromosomal bands, mouse homologies, and much more. Individual items in the tracks opens details pages and provide direct links to othe repositories, such as OMIM, GenBank, PubMed, Entrez, etc, and much more functionality than it is possible to compress into this short description. The binaries are available for download, allowing you to use it for your own genome. The web app contains sequences of over 100 species, including human (Latest: Human assembly is Dec. 2013 [GRCH38/hg38]).


Biology, Genetics


  • Operation: Query and retrieval, Data retrieval, Database search
  • Software interface: Web user interface
  • Language: -
  • License: Binaries and source code are free for academic and nonprofit use.
  • Cost: -
  • Version name: -
  • Maturity: Stable
  • Credit: See
  • Contact:
  • Collection: -


Mangan ME, Williams JM, Kuhn RM, Lathe WC "The UCSC Genome Browser: What Every Molecular Biologist Should Know." Curr Protoc Mol Biol 2014
PMID: 24984850
PMCID: PMC4142428

The Genome Sequencing Consortium. "Initial sequencing and analysis of the human genome." Nature. 2001 Feb 15;409(6822):860-921.
PMID: 11237011

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D "BigWig and BigBed: enabling browsing of large distributed datasets." Bioinformatics 2010; 26(17):2204-7
PMID: 20639541
PMCID: PMC2922891

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ "Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser." Bioinformatics 2014; 30(7):1003-5
PMID: 24227676
PMCID: PMC3967101

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ "The UCSC Table Browser data retrieval tool." Nucleic Acids Res. 2004; 32(Database issue):D493-6
PMID: 14681465
PMCID: PMC308837

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. "ENCODE data in the UCSC Genome Browser: year 5 update." Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63.
PMID: 23193274
PMCID: PMC3531152

Kent WJ, Haussler D "Assembly of the working draft of the human genome with GigAssembler." Genome Res. 2001; 11(9):1541-8
PMID: 11544197
PMCID: PMC311095

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D "The human genome browser at UCSC." Genome Res. 2002; 12(6):996-1006
PMID: 12045153
PMCID: PMC186604

Kent WJ "BLAT--the BLAST-like alignment tool." Genome Res. 2002; 12(4):656-64
PMID: 11932250
PMCID: PMC187518

Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D "Exploring relationships and mining data with the UCSC Gene Sorter." Genome Res. 2005; 15(5):737-41
PMID: 15867434
PMCID: PMC1088302

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