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

Detail

  • 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: -

  • Credit: See https://genome.ucsc.edu/goldenPath/credits.html

  • Input: -

  • Output: -

  • Contact: https://genome.ucsc.edu/contacts.html

  • Collection: -

  • Maturity: Stable

Publications

  • Initial sequencing and analysis of the human genome.
  • Lander ES, et al. Initial sequencing and analysis of the human genome. Initial sequencing and analysis of the human genome. 2001; 409:860-921. doi: 10.1038/35057062
  • https://doi.org/10.1038/35057062
  • PMID: 11237011
  • PMC: -
  • BigWig and BigBed: enabling browsing of large distributed datasets.
  • Kent WJ, et al. BigWig and BigBed: enabling browsing of large distributed datasets. BigWig and BigBed: enabling browsing of large distributed datasets. 2010; 26:2204-7. doi: 10.1093/bioinformatics/btq351
  • https://doi.org/10.1093/bioinformatics/btq351
  • PMID: 20639541
  • PMC: PMC2922891
  • Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.
  • Raney BJ, et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. 2014; 30:1003-5. doi: 10.1093/bioinformatics/btt637
  • https://doi.org/10.1093/bioinformatics/btt637
  • PMID: 24227676
  • PMC: PMC3967101
  • ENCODE data in the UCSC Genome Browser: year 5 update.
  • Rosenbloom KR, et al. ENCODE data in the UCSC Genome Browser: year 5 update. ENCODE data in the UCSC Genome Browser: year 5 update. 2013; 41:D56-63. doi: 10.1093/nar/gks1172
  • https://doi.org/10.1093/nar/gks1172
  • PMID: 23193274
  • PMC: PMC3531152
  • Assembly of the working draft of the human genome with GigAssembler.
  • Kent WJ and Haussler D. Assembly of the working draft of the human genome with GigAssembler. Assembly of the working draft of the human genome with GigAssembler. 2001; 11:1541-8. doi: 10.1101/gr.183201
  • https://doi.org/10.1101/gr.183201
  • PMID: 11544197
  • PMC: PMC311095
  • Exploring relationships and mining data with the UCSC Gene Sorter.
  • Kent WJ, et al. Exploring relationships and mining data with the UCSC Gene Sorter. Exploring relationships and mining data with the UCSC Gene Sorter. 2005; 15:737-41. doi: 10.1101/gr.3694705
  • https://doi.org/10.1101/gr.3694705
  • PMID: 15867434
  • PMC: PMC1088302

Download and documentation

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