For better experience, turn on JavaScript!


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]).

Topic

Biology, Genetics

Details

  • 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 https://genome.ucsc.edu/goldenPath/credits.html
  • Contact: https://genome.ucsc.edu/contacts.html
  • Collection: -

Publications

Mangan ME, Williams JM, Kuhn RM, Lathe WC "The UCSC Genome Browser: What Every Molecular Biologist Should Know." Curr Protoc Mol Biol 2014 https://doi.org/10.1002/0471142727.mb1909s107
PMID: 24984850
PMCID: PMC4142428


The Genome Sequencing Consortium. "Initial sequencing and analysis of the human genome." Nature. 2001 Feb 15;409(6822):860-921. https://doi.org/10.1038/35057062
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 https://doi.org/10.1093/bioinformatics/btq351
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 https://doi.org/10.1093/bioinformatics/btt637
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 https://doi.org/10.1093/nar/gkh103
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. https://doi.org/10.1093/nar/gks1172
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 https://doi.org/10.1101/gr.183201
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 https://doi.org/10.1101/gr.229102
PMID: 12045153
PMCID: PMC186604


Kent WJ "BLAT--the BLAST-like alignment tool." Genome Res. 2002; 12(4):656-64 https://doi.org/10.1101/gr.229202
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 https://doi.org/10.1101/gr.3694705
PMID: 15867434
PMCID: PMC1088302


Download and documentation




You may also like:



If you find errors, please report here.