UCSC Genome Bioinformatics
Genome Browser
Blat
Table Browser
Gene Sorter
In Silico PCR
Genome Graphs
Galaxy
VisiGene
Utilities
Downloads
Release Log
Custom Tracks
Cancer Browser
Microbial Genomes
ENCODE
Neandertal
Mirrors
Training
Blog
Credits
Publications
Cite Us
Licenses
Jobs
Staff
Contact Us

  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 ENCODE data at UCSC (2003 to 2012) and to the Neandertal project. You may download or purchase the Genome Browser source code, or the Genome Browser in a Box (GBiB) at our online store.

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 UC Santa Cruz Genomics Institute 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. The Genome Browser is for research use only. Not intended for clinical use.

The Genome Browser project team relies on public funding to support our work. Donations are welcome -- we have many more ideas than our funding supports! If you have ideas, drop a comment in our suggestion box. Give to the UCSC Genome Browser

  NewsFollow @GenomeBrowser on Twitter Genome Browser Facebook page

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. Please see our blog for posts about Genome Browser tools, features, projects and more.


15 June 2016 - New Official Asian Mirror Released

We are pleased to announce the introduction of a new supported Genome Browser mirror to serve our users in Asia. The genome-asia server (http://genome-asia.ucsc.edu), which is administered by UCSC, is physically located at the RIKEN Yokohama Campus in Japan.

Genome-asia is intended as an alternate, faster access point for those Browser users who are geographically closer to Asia than to the western United States. The mirror is functionally identical to the U.S.-based server, with one exception. Custom tracks residing on the U.S. server are not automatically accessible from the genome-asia mirror; therefore, the use of these custom tracks and saved sessions containing them will require some manual intervention.

Genome Browser users located in Asia will be automatically redirected to genome-asia when they click the "Genomes" menu item on the Genome Browser home page, but will have the option to remain on the U.S.-based server. In addition to the genome-asia mirror, we continue to support a Europe-based Genome Browser mirror (http://genome-euro.ucsc.edu) in Bielefeld, Germany. A third-party mirror in Aarhus, Denmark, is available as an emergency backup in the rare event that our three supported sites are offline.

We wish to express our special thanks to Dr. Hideya Kawaji at the RIKEN Advanced Center for Computing and Communication for making this possible. We would also like to acknowledge the following members of the UCSC Genome Browser team for their efforts: Galt Barber, Robert Kuhn, Jorge Garcia, and Luvina Guruvadoo.


6 June 2016 - New video: Exon-only mode

We are pleased to announce the release to our YouTube channel of a new training video, in which we demonstrate the recently released Multi-Region feature in exon-only mode. This feature is useful for those studying gene expression or undertaking whole-exome sequencing. By removing intronic and intergenic regions, exon-only mode shows the portion (sometimes as little as a few percent) of the genome most useful for these analyses.

This video is indexed to allow easy access to relevant sections and comes with a transcript for the hard-of-hearing.

Thanks to Robert Kuhn and David Gibson for production.


1 June 2016 - New Density Graph Feature!

The Genome Browser is proud to announce a new "density graph" feature for a variety of tracks, including BAM custom tracks, that converts data into a summary display.

The density graph feature enables certain track types to be displayed as a bar graph where the height is proportional to the number of reads mapped to each genomic position. Through dynamic calculation of items in the current window, this feature plots a line similar to a wiggle graph that can be customized with a number of graph-based configuration options such as drawing indicator lines, smoothing plots, adjusting graph height and vertical range, and switching from bars to points. Please note that the feature is best displayed with Display mode set to full and that the default is auto-scale data to view. Please note that using this feature on a virtual machine Genome Browser in a Box (GBiB) may benefit from increasing memory.

To turn on the feature click into the track controls for certain track types, such as a BAM custom track, and check the box next to "Display data as a density graph" to see graph configurations and then click "Submit". To see the new density graph feature in use, please see this example session.

Thanks to Brian Raney for the implementation of this feature.


10 May 2016 - New Gateway Page!: The UCSC Genome Browser team is proud to announce a newly redesigned Genome Browser Gateway page. Please see our Gateway video for an introduction to these new features. Read more.


  Conditions of Use

The Genome Browser software, sequence and annotation data are freely available for use with these conditions. A license is required for commercial use of the software. For assistance with questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles, click here.

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.

The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz. Software Copyright (c) The Regents of the University of California. All rights reserved.