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.

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

Genome Browser and Mailing List Downtime in December

The UCSC campus will be undergoing electrical work from 8:00 am PST Saturday 27 Dec. through 6:00 pm PST Monday 29 Dec. Although the work that is currently planned should not impact access to the Genome Browser, there is a slight possibility that you may lose temporary online access to our tools during this period.

The Genome Browser mailing lists (genome@soe.ucsc.edu and genome-mirror@soe.ucsc.edu) will be down during this time period. Emails sent to the lists will be queued and will be posted when the lists come back online. Note that 24 Dec. through 1 Jan. is a campus holiday, and therefore some questions posted to our list may not receive a response until after the 1 Jan.

The Sep. 2007 EquCab2 release of the horse genome (Equus caballus) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab2, was produced by the Broad Institute.

The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM".

For more details about the current assembly, see the Broad Institute Horse Genome Project page.

Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.

The UCSC Horse Genome Browser was produced by Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

We have updated the initial UCSC Medaka Genome Browser (oryLat1) to correct an error with chrUn in which the gap relationships between the contigs within their ultracontigs were incorrect. Read more.

17 October 2008 - Quality Assurance Engineer Job Opening: The UCSC Genome Browser group has reopened a search for a Quality Assurance engineer: Biological Database Testing and User Support Technician. Applicants should have a strong background in biology and computation, and excellent skills in scientific writing and editing. For details see the job listing.

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.

• Data organization and format
• Terminology