UCSC Genome Bioinformatics
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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 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.


  News

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

20 March 2009 - Two Research Scientist Positions Open

The Center for Biomolecular Science & Engineering (CBSE) invites applications from outstanding PhD- or MD-level scientists for two distinct positions. Applications are due by March 23.

Cancer Genomics Director

We seek an independent, creative scientist with cancer research experience to guide the group in building our cancer genomics data analysis platform into an essential tool for cancer research and an engine for personalized, genome-based cancer treatment. The successful candidate will extend our existing cancer research collaborations, conceptualize new research directions, oversee their implementation by our outstanding postdoctoral students and scientific programming staff, write papers and present results at scientific meetings, and apply for additional grants. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC. Read more.

Medical Genomics Director

We seek an independent, creative scientist who can guide the group in the direction of clinical diagnostics, pediatric/prenatal diagnostics, personalized medicine, pharmacogenomics, or related fields, building on the exceptional genome analysis resources at UCSC. The successful candidate will interface with the medical community, conceptualize genomics projects, oversee implementation by the scientific programming staff, write papers describing the projects, and apply for grants to fund future projects. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC. Read more.


13 March 2009 - ENCODE DCC data available

We'd like to invite everyone to explore UCSC's ENCODE Data Coordination Center website, as well as the ENCODE data displayed as annotation tracks in the UCSC Genome Browser. Today's featured dataset is a track showing transcription factor binding sites determined by ChIP-seq, produced through a collaboration of Yale University, University of CA Davis, and Harvard University. Many more tracks from the Feb. 2009 and Dec. 2008 ENCODE data freezes will become available on the UCSC Genome Browser in upcoming weeks. To monitor the ENCODE data releases in the Genome Browser, see the UCSC ENCODE data release page.


17 February 2009 - Navigate with drag-and-zoom: We would like to announce the release of a new navigation feature, called drag-and-zoom, in the Genome Browser. Read more.


12 February 2009 - v200 code release on Darwin's 200th birthday: As coincidence would have it, we are releasing version 200 of the browser code base this week. Read more.


  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 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.



  Technical Information About the Assembled Sequence