UCSC Genome Browser database

The University of California Santa Cruz (UCSC) Genome Bioinformatics website is a comprehensive resource providing free, open-source on-line tools to browse, analyze, and query genomic data. These tools are available to anyone with an Internet browser and an interest in genomics. The website is designed to cater to the needs of researchers, clinicians, educators, and students, making it a valuable resource for the genomics community.

One of the website's key features is the quick and easy-to-use visual display of genomic data. The UCSC Genome Browser database places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. These annotation tracks are submitted by scientists worldwide, making the database a comprehensive resource that covers a wide range of genomic data. In addition, the UCSC Genome Bioinformatics group computes annotation tracks from publicly available sequence data, further enhancing the database's coverage.

The UCSC Genome Browser database allows users to upload and display their experimental results or annotation sets by creating a custom track. This feature enables researchers to share their findings with the wider scientific community, facilitating collaborations and advancing research in the field of genomics. The custom track option also enables researchers to visualize their data alongside publicly available datasets, providing a unique opportunity to gain novel insights and generate new hypotheses.

Overall, the UCSC Genome Browser database is a valuable resource for anyone interested in genomics. Its suite of tools, downloadable data files, and links to documentation and other information make it an indispensable tool for researchers, clinicians, educators, and students alike. The website's commitment to open-source and free resources reflects its mission to facilitate the advancement of research in the field of genomics.

Topic

Model organisms;Genotype and phenotype;Data visualisation;Data integration and warehousing;Genomics

Detail

  • Operation: Database search;PCR primer design;Genome visualisation;Sequence alignment;Genetic variation analysis

  • Software interface: Database portal

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI) and the National Cancer Institute (NCI), HHMI Predoctoral Fellowship.

  • Input: -

  • Output: -

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

  • Collection: -

  • Maturity: Mature

Publications

  • UCSC genome browser: deep support for molecular biomedical research.
  • Mangan ME, et al. UCSC genome browser: deep support for molecular biomedical research. UCSC genome browser: deep support for molecular biomedical research. 2008; 14:63-108. doi: 10.1016/S1387-2656(08)00003-3
  • https://doi.org/10.1016/S1387-2656(08)00003-3
  • PMID: 18606360
  • PMC: -
  • The UCSC Genome Browser Database: update 2006.
  • Hinrichs AS, et al. The UCSC Genome Browser Database: update 2006. The UCSC Genome Browser Database: update 2006. 2006; 34:D590-8. doi: 10.1093/nar/gkj144
  • https://doi.org/10.1093/nar/gkj144
  • PMID: 16381938
  • PMC: PMC1347506
  • The UCSC genome browser database: update 2007.
  • Kuhn RM, et al. The UCSC genome browser database: update 2007. The UCSC genome browser database: update 2007. 2007; 35:D668-73. doi: 10.1093/nar/gkl928
  • https://doi.org/10.1093/nar/gkl928
  • PMID: 17142222
  • PMC: PMC1669757
  • The UCSC Genome Browser Database: 2008 update.
  • Karolchik D, et al. The UCSC Genome Browser Database: 2008 update. The UCSC Genome Browser Database: 2008 update. 2008; 36:D773-9. doi: 10.1093/nar/gkm966
  • https://doi.org/10.1093/nar/gkm966
  • PMID: 18086701
  • PMC: PMC2238835

Download and documentation


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