UCSC Genome Bioinformatics
Genome Browser
Table Browser
Gene Sorter
In Silico PCR
Genome Graphs
Release Log
Custom Tracks
Cancer Browser
Microbial Genomes
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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 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.

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. The Gateway retains its original functionality as a central access point for all genome assemblies available on our site, while sporting several helpful new features and updates:

  • Autocomplete searching for any genome browser, genome version, or public hub
  • Species browsing through a scrollable visual "tree" menu based on phylogenetic order
  • Quick access shortcuts to popular browsers
  • New style and color scheme

Please see our Gateway video for an introduction to these new features.

The new Gateway addresses the need for streamlined access to the rapidly growing number of genome assemblies available on our public site. As an alternative to scrolling through long drop-down menus of genome assemblies, you can now simply type in assembly search terms for autocomplete recognition, visually scroll through our collection, or click a button to access our most popular species.

Note that a few browser utilities that were previously accessed through links and buttons on the Gateway page have been moved to the top menu bar:

  • Browser reset: Genome Browser > Reset All User Settings
  • Track search: Genome Browser > Track Search
  • Add custom tracks: My Data > Custom Tracks
  • Track hubs: My Data > Track Hubs
  • Configure tracks and display: Genome Browser > Configure

We would like to acknowledge the following people for their contributions to the new Gateway: original art by Jeff West Design, concept by Robert Kuhn, software design by Angie Hinrichs, and quality assurance by Cath Tyner.

22 Apr 2016 - Data from the Lens PatSeq Database Now Available: We are pleased to announce the release of a set of tracks containing data from the Lens PatSeq database in the UCSC Genome Browser. 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.