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  About the UCSC Genome Bioinformatics Site

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.




  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.


8 August 2006 - New Opossum Assembly Available in Genome Browser


The UCSC Genome Browser now includes the latest draft assembly of the opossum genome. The Jan. 2006 release of Monodelphis domestica (UCSC version monDom4) was sequenced and assembled by The Broad Institute, Cambridge, MA, USA.


This draft, which has approximately 6.5X coverage, has an assembly length of nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, and Un. The N50 of the genome including gaps is 104,359 bp; the N50 without gaps is 107,990. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.


The monDom4 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. Please review the guidelines for using the opposum assembly data.


Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to the release of this browser.


1 August 2006 - v2.1 Chicken Assembly Available in Genome Browser: We have updated the Chicken Genome Browser to include the May 2006 v2.1 assembly (UCSC version galGal3) produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL). Read more.

20 July 2006 - New Chimpanzee Genome Browser Released: We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. Read more.




  Conditions of Use

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.


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

Description of the annotation database

Data organization and format

Terminology




  Related Links

Center for Biomolecular Science and Engineering Home Page

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