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
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
to allow easy access to relevant sections and comes with a transcript for the
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
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
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
PatSeq database in the UCSC Genome Browser.