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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.
1 Apr 2016
- Going Back to Our Roots
For many years, the UCSC Genome Browser has provided a dynamic, cutting-edge
interface for
viewing genomic data. As time has gone by, however, it has become clear to us
that we
cannot keep this up. It is not fair to you, our users, that our interface
keeps changing,
and it has increasingly been a burden on us to keep up with emerging web
technologies. Today
that all changes, as we return you to the roots of the web: ASCII.
We apologize again for subjecting you to so many changes over the years, and
hope that this
new, more consistent interface will find your approval.
In related news, we have also revised the interface for uploading custom
tracks. Rather than
forcing you to wrestle with inconvenient file formats for your data or attempt
to set up a web server,
we now provide the option of loading your data from a deck of ISO 6586:1980
punch cards. Simply
punch your data onto a deck and mail the deck to us. Our staff of highly
trained specialists
will take care of loading track, and will inform you by mail when the process
is complete. Please
note that our current policy of expiring unused custom tracks remains in
effect; you must visit
your track within 72 hours of the postmark date. Regrettably, decks cannot be
returned.
Card decks may be addressed to:
UCSC Genome Informatics Group
Center for Biomolecular Science & Engineering
CBSE, 501D Engineering II Building
University of California, Santa Cruz
1156 High Street
Santa Cruz, CA 95064
This new file format is also an option for data output from the UCSC Table Browser.
Simply select "mail card deck" from the "output format" menu, and then enter
your name and address on the subsequent
page. Please allow 4-6 weeks for delivery.
21 Mar 2016
- Genome Browsers for C. elegans and Brown Kiwi Now Available
A Genome Browser is now available for the Caenorhabditis elegans
assembly released February 2013 by the C. elegans Sequencing Consortium
(C. elegans Sequencing Consortium version WBcel235, UCSC version ce11).
For more information and statistics about this assembly, see the NCBI assembly record
for WBcel235.
There are 7 complete chromosomes with a total size of 100,286,401 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
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A Genome Browser is now available for the brown kiwi (Apteryx australis)
assembly released June 2015 by the
Max-Plank Institute for Evolutionary Anthropology (MPI-EVA version AptMan0,
UCSC version aptMan1).
For more information and statistics about this assembly, see
AptMant0 in the NCBI Assembly database. There are
24,719 scaffolds with a total size of 1,523,986,457 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
FTP server or the
Downloads page.
Please observe the conditions for use when
accessing and using these data sets. The annotation tracks for this browser were
generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the
organizations and individuals who contributed to this release.
8 Mar 2016
- Combine Multiple Regions of the Genome Browser into a Single Visualization!
Have you ever wished you could remove all of the intronic or intergenic regions from the
Genome Browser display? Have you ever dreamed of being able to visualize multiple
far-flung regions of a genome? Well, now you can with the new "multi-region" option
in the Genome Browser!
The multi-region modes provide four different ways to manipulate the display.
First, we have an "exon-only" mode that allows you to
remove all of the intergenic and intronic sequences from the display, leaving you with
only the exonic regions. Next, there is the "gene-only" mode allowing you to remove only
the intergenic regions from the display, leaving the genes with exons and introns intact.
Then there is the "custom regions" mode that allows you to use a remote BED file to
specify the regions you are interested in viewing alongside each other. Lastly, for human
assemblies hg17 and newer, there is the "alternative haplotype" mode that allows you to
view a haplotype sequence inserted into its position in the reference genome.
To access these exciting, new multi-region modes, first select your organism and assembly
of interest and navigate to the Genome Browser visualization. Below the tracks display,
there is a button labeled "multi-region". Clicking this button will bring up
a configuration box for the different multi-region modes. For example:
From this pop-up, you will be able to switch between the different modes or exit these
multi-region modes if desired. For instance:
Additionally, you can enter the "Exon-only" mode by typing the keyboard shortcut
"e" then "v". You can exit any of the multi-region modes and return to the
default Genome Browser display by typing the keyboard shortcut "d" then "v".
For more information about each individual multi-region mode, please see the
User Guide.
Thank you to Galt Barber, Matthew Speir, and the entire UCSC Genome Browser quality assurance team for
all of their efforts in creating these exciting new display modes.
10 February 2016 -
Two New Assemblies Now Available in the Genome Browser:
Genome Browsers are now available for the mouse lemur
(Microcebus murinus)
and platypus (Ornithorhynchus anatinus) assemblies.
Read more.
20 Jan 2016 —
dbSNP 142 Available for mm10
Read more.
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