UCSC Genome Browser Home

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Last full update: Fri Feb 5 08:50:00 2010

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 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.

News

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

25 Jan. 2010 - New Custom Track type: Binary Alignment/Map (BAM)

We are pleased to announce the availability of another new track type for Custom Tracks: the Binary Alignment/Map (BAM).

BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the BAM file and its associated index file remain on your web-accessible server (http or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display.

13 Jan. 2010 - Lifespan of custom tracks within sessions: Due to the popularity of UCSC custom tracks and sessions, we are running out of disk space for storing custom tracks accessed within sessions. Although sessions themselves are saved for one year, user-generated tracks within sessions (including custom tracks) are saved for 48 hours, the typical period for other custom tracks. Until now, because we have had space available on the server, we have attempted to keep custom tracks alive for the lifetime of the session. Read more.

11 Jan. 2010 - Zebrafish release zv8 now available in Genome Browser: The most recent zebrafish assembly -- zv8 (UCSC version danRer6, Dec. 2008) -- is now available in the UCSC Genome Browser. This assembly was produced by the Wellcome Trust Sanger Institute, UK. Read more.

14 Dec. 2009 - New job posting: Biological Data Technician: The UCSC Genome Browser project is looking for a bioinformatician, biologist, or software engineer with a strong biology background to collect and import data into the UCSC Genome Browser database and website. Read more.

7 Dec. 2009 - Human Genome Browser default changing to hg19: In conjunction with the release of the UCSC Genes and Conservation tracks on the hg19 (GRCh37) human assembly, we have changed the default human browser on our website from hg18 to hg19. 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.

Technical Information About the Assembled Sequence


Data organization and format Terminology