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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.

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.


  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.

22 July 2013 - Variant Annotation Integrator

In order to assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed the Variant Annotation Integrator (VAI). Given a set of variants uploaded as a custom track (in either pgSnp or VCF format), the VAI will return the predicted functional effect (e.g., synonymous, missense, frameshift, intronic) for each variant. The VAI can optionally add several other types of relevant information, including: the dbSNP identifier if the variant is found in dbSNP, protein damage scores for missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP), and conservation scores computed from multi-species alignments. The VAI also offers filters to help narrow down results to the most interesting variants.

Future releases of the VAI will include more input/upload options, output formats, and annotation options, and a way to add information from any track in the Genome Browser, including custom tracks.

There are two ways to navigate to the VAI: (1) From the "Tools" menu, follow the "Variant Annotation Integrator" link. (2) After uploading a custom track, hit the "go to variant annotation integrator" button. The user's guide is at the bottom of the page, under "Using the Variant Annotation Integrator."

Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and Jonathan Casper for their input and work on this feature.

2 July 2013 - Assembly Data Hubs

We are pleased to announce a new feature in the UCSC Genome Browser: Assembly Data Hubs.

Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. Assembly Data Hubs were developed to address the increasing need for researchers to annotate sequence for which UCSC does not provide an annotation database. They allow researchers to include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are stored in the same manner as Track Data Hubs.

To read more about using Assembly Data Hubs, or about creating your own, please see these guides:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature.


2 July 2013 - New Gene Alleles feature on the details pages of UCSC genes: For each protein-coding gene in the UCSC Genes track, variant data from the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000 Genomes Project have been distilled into "gene haplotype alleles." Read more.

28 June 2013 - New UCSC Genes Track Released for GRCh37/hg19: We're happy to announce the release of an updated UCSC Genes track for the GRCh37/hg19 human Genome Browser. Read more.

27 June 2013 - New Official European Mirror Released: Announcing an official mirror for European users, with automatic redirection. Read more.

26 June 2013 - Suggestion Box Released: Due to popular demand, we have created a suggestion box for track, assembly, tool, and other feature requests. 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 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.