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 have released a Genome Browser for the September 2009 genome assembly of the Tammar Wallaby, Macropus eugenii (TWGS version Meug_1.1, UCSC version macEug2). This assembly, which has been sequenced to 2X coverage, was produced by the Tammar Wallaby Genome Sequencing Consortium, a collaboration between the Baylor College of Medicine Human Genome Sequencing Center and the Australian Genome Research Facility.

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.

We'd like to thank the Tammar Wallaby Genome Sequencing Consortium for providing this assembly. The wallaby Genome Browser and annotation tracks were produced by Chin Li and Luvina Guruvadoo. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington University

We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our Data Hub function. The Roadmap Epigenomics Project is part of The NIH Common Fund's Epigenomics Program. It was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. The Consortium expects to deliver a collection of normal epigenomes that will provide a framework or reference for comparison and integration within a broad array of future studies.

All data were produced and processed by the Roadmap Epigenomics Mapping Consortium, and will be periodically updated. Genome Browser tracks were constructed and hosted by VizHub at Washington University in St. Louis. Tracks are available at UCSC Genome Browser via the Data Hub function, or follow this link. The Roadmap Epigenomics Mapping Consortium is responsible for the quality of the data.

19 December 2011 - Variant Call Format (VCF) Now Supported in Genome Browser

We are pleased to announce that the UCSC Genome Browser now supports Variant Call Format (VCF). VCF is a flexible and extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants and structural variants discovered by the project. Similar to bigBed, bigWig and BAM, the Browser transfers only the portions of VCF files necessary to display viewed regions, making VCF a fast and attractive option for large data sets. VCF files will need to be compressed and indexed using the tabix package available from SAMtools. This new format is available for use in custom tracks and data hubs. For more information about VCF and tabix, please see our VCF Track Format help page.

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. Read more.

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.

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.