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  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 portals to the ENCODE and Neandertal projects.

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.


  NewsFollow GenomeBrowser on Twitter

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

7 November 2011 - UMD Cow Assembly Now Available in Genome Browser

In response to the many requests from the bovine research community, we now offer the University of Maryland (UMD) Bos taurus assembly in the Genome Browser, in addition to the assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center. The UMD v3.1 assembly (Nov. 2009, UCSC bosTau6) was produced by the UMD Center for Bioinformatics and Computational Biology (CBCB) in College Park, MD.

The UMD 3.1 assembly is based on reads downloaded from the NCBI Trace Archive, most of which were sequenced by the Baylor College of Medicine. UMD reports that they were able to apply several assembly improvement techniques to produce an assembly that is substantially more accurate and complete than previous alternative versions, as evaluated using independent metrics. Based on UMD statistics, this assembly provides more genome coverage, closes thousands of gaps, corrects many erroneous inversions, deletions, and translocations, and fixes thousands of single-nucleotide errors. For more information, see Zimin AV et al, A whole-genome assembly of the domestic cow, Bos taurus, Genome Biol. 2009;10(4) and the UMD CBCB Bos taurus assembly web page.

Downloads of the UMD bovine data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page.

We'd like to thank the UMD CBCB for providing this genome assembly. The UMD Cow Genome Browser and annotation tracks were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.


10 October 2011 - Updated Yeast Browser Released: We are happy to announce the release of an updated browser for the Saccharomyces cerevisiae yeast genome. Read more.

8 September 2011 - New Navigation and Display Features: We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. Read more.

18 August 2011 - New Feature: Track Data Hubs: We are pleased to announce a new feature in the UCSC Genome Browser: Track Data Hubs. Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Read more.

==> News Archives

  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 UCSC, Ensembl, and NCBI browser and annotation groups have established a common set of minimum requirements for public display of genome data made available after Spring 2009, described here.

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.