This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also shows the CFTR (cystic fibrosis) region in 13 species and 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.

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

Status of hg17 SNP Track

The UCSC Genome Browser SNP track is based on data from NCBI's dbSnp. We have recently downloaded the SNP data for the latest human genome assembly (hg17, May 2004) and are generating the annotation track. We should have the data available on the Genome Browser by approximately the end of the fourth week in November.

The v.3.0 Xenopus tropicalis assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro1, October 2004) was provided by the U.S. DOE Joint Genome Institute (JGI).

Version 3.0 was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half the genome is contained in 392 scaffolds, each of which is at least 1.2 Mb in length. For more information about this assembly, see the JGI X. tropicalis website.

The xenTro1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please see the JGI data release policy for data use guidelines.

Many thanks to JGI and the other institutions who contributed to the sequencing and mapping effort of the v. 3.0 release. The UCSC X. tropicalis Genome Browser was produced by Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik. The initial set of xenTro1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.

17 November 2004 - Genome Browser Tutorial Offered at ASCB Meeting on 5 Dec.

OpenHelix will be presenting the tutorial "Introduction to the UCSC Genome Browser" at the American Society for Cell Biology (ASCB) Annual Meeting in Washington, D.C. on 5 Dec., 8:30 - 10:00 p.m. This introductory session will cover the topics needed to effectively use the Genome Browser, including basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter.

The free 1-1/2-hour tutorial will be conducted at the Washington Convention Center, Room 206. OpenHelix will also be presenting brief introductory overviews of the UCSC Genome Browser in its ASCB booth #510-512 during show hours. Stop by the booth for more information and to receive your free UCSC Quick Reference Card.

For more information about the tutorial and other services offered by OpenHelix, visit www.openhelix.com or call 1-888-861-5051.

5 October 2004 - East Coast Genome Browser Seminars in November: The UCSC Bioinformatics Group announces two seminars and hands-on workshops on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. Read more.

1 October 2004 - New Table Browser Released: We are pleased to announce the release of an enhanced version of the UCSC Table Browser. Read more.

The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal 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.

Questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles should be sent to genome@soe.ucsc.edu. Messages sent to this address will be posted automatically on the genome mailing list, which is also archived on a public Web-accessible pipermail archive. NOTE: This archive may be indexed by non-UCSC sites such as Google.

• Description of the annotation database
• Data organization and format
• Terminology

• Center for Biomolecular Science and Engineering Home Page