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.

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

11 February 2013 - Denisova tracks released on hg19 browser
In conjunction with the publication of the paper by Meyer et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual the UCSC Genome Browser is hosting a set of new tracks. Briefly, Meyer et al. applied a novel single-stranded DNA library preparation method to DNA previously extracted from 40mg of a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia.

Two supporting datasets and one analysis dataset are now available in the Genome Browser:

• Modern Human Variants: variant calls made from sequence reads of eleven individuals mapped to the human genome, used in statistical analyses to put the divergence of the Denisova genome into perspective with regard to present-day humans.
• Denisova Sequence: high-coverage (30X) sequence reads from an archaic Denisovan individual mapped to the human genome reference assembly.
• Modern Human Derived, Denisova Ancestral: mutations in the modern human lineage that rose to fixation or near fixation since the split from the last common ancestor with Denisovans, along with predicted functional effects from Ensembl's Variant Effect Predictor (VEP).

We'd like to thank Richard Green and the many authors of the Science paper for providing the UCSC Genome Browser with these data. We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the annotations and information for these tracks: Angie Hinrichs and Pauline Fujita.

25 January 2013 - Southern White Rhinoceros Genome Browser Release: We are pleased to announce the release of a Genome Browser for the May 2012 assembly of the Southern White Rhinoceros, Ceratotherium simum simum (Broad Institute version cerSimSim1.0, UCSC version cerSim1). Read more.

22 January 2013 - New Baboon (papAnu2) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the March 2012 assembly of the Olive Baboon, Papio anubis (Baylor Panu_2.0, UCSC version papAnu2). Read more.

15 January 2013 - New Lamprey (petMar2) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the September 2010 assembly of the Lamprey, Petromyzon marinus (WUGSC 7.0, UCSC version petMar2). 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.