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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.

10 October 2011 - Updated Yeast Browser Released

We are happy to announce an updated Yeast Genome Browser for Saccharomyces cerevisiae, sacCer3. The April 2011 Saccharomyces cerevisiae genome assembly (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database (GCA_000146055.2)) was produced by the Saccharomyces Genome Database (SGD™) project.

Chromosomes available in this assembly: chrI, chrII, chrIII, chrIV ... etc ... chrXVI, and chrM. See also: SGD™ genome snapshot/overview.

Downloads of the yeast data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The S. cerevisiae annotation tracks were generated by UCSC and collaborators worldwide.

We'd like to thank the Saccharomyces Genome Database (SGD™). The S. cerevisiae Genome Browser and annotation tracks were produced by Hiram Clawson, Greg Roe, and Steve Heitner. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

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.

Automatic image resizing: The first time the annotation track window is displayed, or after the Genome Browser has been reset, the size of the track window is now set by default to the width that best fits your Internet browser window. If you subsequently resize your browser window, you can automatically adjust the annotation track image size to the new width by clicking the resize button under the track image. The default width can still be manually overridden on the Track Configuration page.

Scrolling left or right in the track window: You can now scroll (pan) horizontally through the tracks image by clicking on the image, dragging the cursor to the left or right, then releasing the mouse button. The view may be scrolled by up to one image width.

Improved drag-zoom navigation: The browser's "drag-and-zoom" feature lets you quickly zoom to a specific region of interest on the annotation tracks image. To define the region you wish to zoom to, depress the shift key, click-and-hold the mouse button on one edge of the desired zoom area (which can be anywhere in the tracks window), drag the mouse right or left to highlight the selection area, then release the mouse button. The annotation tracks image will automatically zoom to the new region. The Genome Browser still supports the earlier implementation of this feature, which restricted the click-drag to the Base Position track area of the image, but did not require the shift key to be pressed.

Reordering groups of tracks: You can now vertically reposition an entire group of associated tracks in the tracks image (such as all the displayed subtracks in a composite track) by clicking and holding the gray bar to the left of the tracks, dragging the group to the new position, then releasing the mouse button. To move a single track up or down, click and hold the mouse button on the side label, drag the highlighted track to the new position, then release the mouse button.

If you haven't yet tried the browser's right-click menu for quick access to frequently used track configuration features and functionality, read more here.

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.