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.

WARNING: This is a test site. Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. For high-quality reviewed annotations on our production server, visit http://genome.ucsc.edu.

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

We are pleased to announce the release of a Genome Browser for the October 2011 fugu, Takifugu rubripes (JGI v5.0, UCSC version fr3). Whole genome shotgun assembly was provided by the International Fugu Genome Sequencing Consortium, led by JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The fugu (fr3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.

We are pleased to announce the release of a Genome Browser for the July 2011 naked mole-rat, Heterocephalus glaber (BGI version HetGla1.0, UCSC version hetGla1). This draft assembly, produced by the Beijing Genomics Institute, has been sequenced using Illumina reads with a sequencing depth of >20x. There are 39,266 scaffolds with a total size of 2,643,961,837 bases. The N50 size of the scaffolds is 1,321,980,918 bases with 502 scaffolds larger, and 38,764 scaffolds smaller. The mitochondrial sequence is also available as the virtual chromosome "chrM".

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The naked mole-rat browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.

OpenHelix is conducting two free webinars on the UCSC Genome Browser:

• UCSC Genome Browser: An Introduction (Thursday, May 17, 1pm EDT) -- designed for new users of the UCSC Genome Browser and those who want to improve their skills at basic navigation and display.
• UCSC Table Browser and Custom Tracks (Thursday, May 24, at 1pm EDT) -- advanced Genome Browser topics, including creating Custom Tracks and using the Table Browser.

The webinars will last approximately 1hr 15min.

Seating is limited and registration is required. Slides may be downloaded from the OpenHelix website prior to the webinar.

OpenHelix provides training materials and programs on hundreds of free, publicly accessible bioinformatics and genomics resources. To browse their entire collection of UCSC genomics tutorials, go to the OpenHelix UCSC training page.

18 April 2012 - GRC Planning Phase for GRCh38 Human Reference Assembly: The Genome Reference Consortium (GRC) plans to update the human reference assembly to GRCh38 in the summer of 2013. Read more.

==> News Archives

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.