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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.

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.

6 May 2010 - UCSC Hosts Portal for Neandertal Sequence, Alignments, and Analyses

In conjunction with the publication of the paper Green et al. A Draft Sequence of the Neandertal Genome in the May 7 issue of Science, the UCSC Genome Browser project has released a public Neandertal portal that may be used to access the Neandertal sequence, alignments to the UCSC hg18 (NCBI Build 36) human reference assembly and the UCSC panTro2 (Chimpanzee Sequencing and Analysis Consortium v2.1) chimpanzee reference assembly, and several associated analyses.

Neandertals are the closest extinct relatives of humans. They lived in much of Europe and western Asia before disappearing from the fossil records approximately 30,000 years ago. The Neandertal genome sequence consists of short sequence fragments, usually about 50 base pairs long, mapped to the human reference genome. The sequence was derived primarily from DNA extracted from three Neandertal bones, each about 40,000 years old, found in the Vindija Cave in Croatia; smaller amounts of data were also obtained from three bones from other sites. The bulk sequencing was carried out on the Illumina GAII platform. Neandertal DNA was differentiated from the background of microbial sequences in the bone by similarity to the human or chimpanzee genomes.

The draft sequence of the Neandertal genome yields important new insights into the evolution of modern humans. Among the findings discussed in the Science publication is evidence that some early modern humans, after their migration out of Africa, interbred with Neandertals, resulting in traces of Neandertal DNA sequences in the genomes of present-day non-Africans. The authors also cataloged genetic features unique to modern humans by comparing the Neandertal, human, and chimpanzee genomes. Among the genes highlighted in the study as likely to have undergone important changes in recent human evolution are those involved in cognitive development, skull structure, energy metabolism, skin morphology and physiology.

We'd like to thank Richard Green (formerly of the Max-Planck Institute, and now an assistant professor of biomedical engineering at UCSC) 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 the UCSC Neandertal portal: Angie Hinrichs, Katrina Learned, and Pauline Fujita.

12 May 2010 - Pig Genome Browser Released: We have released a Genome Browser for the pig, Sus scrofa. Read more.

26 Apr. 2010 - European Rabbit Genome Browser Released: We have released a Genome Browser for the European rabbit, Oryctolagus cuniculus. Read more.

16 Apr. 2010 - Giant Panda Genome Browser Released: We have released a Genome Browser for Ailuropoda melanoleuca. 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.