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 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. 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.

The UCSC Genome Browser project is currently accepting applications for a Biological Database Testing/User Support Technician (Programmer/Analyst I). We are looking for a talented self-motivated individual who would like to use their skills in computer science, biology, and bioinformatics on a fast-paced project featuring the work of top genomics scientists worldwide.

For a summary of the position details and qualifications, see Biological Database Testing/User Support Technician on the Center for Biomolecular Science and Engineering (CBSE) website. For detailed job descriptions and application information, go to the UCSC Staff Employment website, click the "Search Postings" link on the sidebar, and type in job #0902365 (Testing/User Support Technician).

If you have been taking advantage of the new bigBed format (for very large data sets), you'll be happy to hear that we have considerably slimmed down the memory footprint of the program that converts BED files into bigBed files: bedToBigBed. Because it now uses a multi-pass approach, it now takes only 1/4 the amount of RAM as the size of the uncompressed BED input file (instead of the 5x RAM it needed previously!). Read more here. Pick up the new bedToBigBed executable here.

In conjunction with this change, there is also a change to the way you must specify your bigBed or bigWig Custom Track. When you specify the location of your local bigBed/bigWig file (on your web-accessible http, https, or ftp server), use this designation: bigDataUrl (instead of the old designation: dataUrl).

Additionally, we would like to announce a companion program to the previously-announced wigToBigWig program: bedGraphToBigWig. This program converts bedGraph files into bigWig files. The bedGraph format allows display of sparse or varying-size data. Read more here. You can download the new bedGraphToBigWig utility here.

The main advantage of the bigBed and bigWig formats is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets, displaying bigBed/bigWig data is considerably faster than regular BED/wig data. The bigBed/bigWig file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Consequently, creating your Custom Track is very fast. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached at UCSC as a "sparse file".

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.

• Data organization and format
• Terminology