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.

27 August 2008 - Zebra Finch Genome Browser Released

We've added the Jul. 2008 release of the zebra finch genome (Taeniopygia guttata) to our collection of vertebrate genome browsers. The v3.2.4 draft assembly (UCSC version taeGut1) was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine in St. Louis, MO, USA.

The zebra finch genome is the second bird genome to be sequenced (following the chicken, Gallus gallus). The DNA used for the shotgun sequencing and the BAC and cosmid libraries was derived from a single male zebra finch. The initial assembly was generated using PCAP with approximately 6X coverage. About 1.0 Gb of the 1.2-Gb genome has been ordered and oriented along 33 chromosomes and one linkage group. The chromosome names are based on their homologous chromosomes in the chicken (Gallus gallus). For more assembly details, as well as a cross reference table of zebra finch and chicken chromosome names, see the WUSTL assembly notes.

Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. These data have specific conditions for use. Please refer to the WUSTL data use policy for additional usage guidelines and citation information.

The UCSC Zebra Finch Genome Browser and initial annotations were produced by Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

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