UCSC Genome Bioinformatics
   Genomes  -   Blat  -   Tables  -   Gene Sorter  -   PCR  -   VisiGene  -   Proteome  -   Session  -   FAQ  -   Help
Genome Browser
ENCODE
Blat
Table Browser
Gene Sorter
In Silico PCR
Genome Graphs
Galaxy
VisiGene
Proteome Browser
Utilities
Downloads
Release Log
Custom Tracks
Archaeal Genomes
Mirrors
Archives
Training
Credits
Publications
Cite Us
Licenses
Jobs
Staff
Contact Us

  About the UCSC Genome Bioinformatics Site

Welcome to the UCSC Genome Browser website. This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.

We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets.

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC). If you have feedback or questions concerning the tools or data on this website, feel free to contact us on our public mailing list. To view the results of the Genome Browser users' survey we conducted in May 2007, click here.


  News

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list.

17 September 2008 - Seven Assemblies Archived

We have archived seven older assemblies of the human (hg15), mouse (mm5, mm6), rat (rn2), C. elegans (ce1), zebrafish (danRer2), and cow (bosTau1) genomes. You can continue to browse these assemblies on the Genome Browser archive server. At least two later assemblies for each of these organisms remain available on the main Genome Browser site.

We do not provide blat servers or updated GenBank data for archived assemblies. However, it is still possible to lift coordinates between these assemblies and those on the main browser site.


15 September 2008 - Request for Input on ENCODE Data Release Plan: The National Human Genome Research Institute (NHGRI) has updated the data release plan for the ENCODE and model organism ENCODE (modENCODE) projects. Because the plan is intended to take into account the needs and responsibilities of the resource users, NHGRI is soliciting feedback on the proposal from the research community before the plan is finalized. To facilitate this review, UCSC has made the plan available to the community here on our ENCODE website. Please send comments directly to Encode@mail.nih.gov by Wednesday, October 15, 2008.

3 September 2008 - Updated UCSC Genes Set Released for hg18: We have released an updated UCSC Genes data set on the latest human assembly (hg18, March 2006). Read more.


  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for any use with the following conditions:

  • Genome sequence data use restrictions are noted within the species sections on the Credits page.
  • Some annotation tracks contributed by external collaborators contain proprietary data that have specific use restrictions. To check for restrictions associated with a particular genome assembly, review the database/README.txt file in the assembly's downloads directory.

The Genome Browser and Blat software are free for academic, nonprofit, and personal use. A license is required for commercial use. See the Licenses page for more information.

Program-driven use of this software is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

For assistance with questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles, see the FAQ.



  Technical Information About the Assembled Sequence