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06 July 2012 - hgText CGI
To Be Retired
We are announcing the imminent retirement of the hgText
CGI. hgText was the original version of the Table Browser,
- and was replaced by the new CGI, hgTables, in 2004. A very
+ and was replaced by the new CGI, hgTables, in 2004. A very
small number of our users are still accessing the database
using the old hgText CGI. Beginning July 24, 2012, we will
be removing the hgText CGI from our site. All users will need
to use hgTables after that time.
19 June 2012 - Many New
Assemblies Available in the Browser!
With the abundance of new vertebrate assemblies available in
GenBank, the UCSC Genome Browser team has streamlined its
browser release pipeline in the effort to keep pace. In the past
week we have released a new browser on the Western painted
turtle and updated assemblies for the cow, rat, and chicken.
Browsers for the lesser hedgehog tenrec and the latest dog
assembly should be available later this week, for a total of 18
assemblies released in the past half year. You can
expect many new assemblies to show up on our website in upcoming
months, along with broader multiple alignment annotations on
selected organisms that include many of the new assemblies.
Keep in mind that some of these new assemblies may not yet be
fully populated with annotation tracks. Some data, such as the
data underlying genes and SNPs tracks, may not be immediately
available, and other annotations (e.g., comparative genomics
tracks) may take a while to generate. As always, our mandated
focus is on vertebrates, with a particular emphasis on richly
annotating the human genome, although we do provide occasional
updated assemblies for other selected model organisms (fly,
worm, yeast).
We regret that we don't have the resources to support the many
other genomics research communities who would like us to
visualize their data in our browser, but we can provide you
with information for setting up your own browser or track hub
to display your data, as well as links to other visualization
resources on the web that are specific to your genome of
interest. Feel free to contact us
for more information.
Newly released assemblies:
- Cow (Bos taurus) bosTau7 –
Btau_4.6.1 (Oct. 2011) from the Bovine Genome Sequencing
Consortium and Baylor College of Medicine
- Rat (Rattus norvegicus) rn5 –
RGSC Rnor_5.0 (Oct. 2011) from the Rat Genome Sequencing
Consortium
- Chicken (Gallus gallus) galGal4
– Gallus_gallus-4.0 (Nov. 2011) from the International
Chicken Genome Consortium
- Western painted turtle (Chrysemys picta bellii)
chrPic1 – Chrysemys_picta_bellii-3.0.1 (Dec. 2011)
from the International Painted Turtle Genome Sequencing Consortium
- Lesser hedgehog tenrec (Echinops telfairi)
echTel1 – echTel1 (Jul. 2005) from the Broad
Institute (pending)
- Dog (Canis familiaris) canFam3
– v3.1 (Sep. 2011) from the Broad Institute (pending)
Released in the past half year:
- Mouse (Mus musculus) mm10 –
GRCm38 (Dec. 2011) from the Mouse Genome Reference Consortium
- Cow (Bos taurus) bosTau6 –
Bos_taurus_UMD_3.1 (Nov. 2009) from the University of Maryland
- Fugu (Takifugu rubripes) fr3 –
FUGU5 (Oct. 2011) from the International Fugu Genome Sequencing
Consortium
- Gibbon (Nomascus leucogenys) nomLeu1
– Nleu1.0 (Jan. 2010) from the Gibbon Genome Sequencing
Consortium
- Gorilla (Gorilla gorilla gorilla) gorGor3
– gorGor3.1 (May 2011) from the Wellcome Trust Sanger
Institute
- Microbat (Myotis lucifugus) myoLuc2
– Myoluc2.0 (Jul. 2010) from the Broad Institute
- Naked mole-rat (Heterocephalus glaber)
hetGla1 – HetGla_1.0 (Jul. 2011) from the Beijing
Genomics Institute
- Tammar wallaby (Macropus eugenii) macEug2
– Meug_1.1 (Sep. 2009) from the Tammar Wallaby Genome
Sequencing Consortium
- Turkey (Meleagris gallopavo) melGal1
– Turkey_2.01 (Dec. 2009) from the Turkey Genome Consortium
- Western clawed frog (X. tropicalis)
xenTro3 – v4.2 (Nov. 2009) from the DOE Joint
Genome Institute
- C. elegans ce10 – WS220
(Oct. 2010) from WormBase
- S. cerevisiae sacCer3 –
SacCer_Apr2011 (Apr. 2011) from the Saccharomyces Genome Database
Bulk downloads of the sequence and annotation data for these
assemblies are available via the Genome Browser
FTP server or the
Downloads page. Be sure to check the
credits
page for data use restrictions and acknowledgments.
Many thanks to the sequencing and assembly groups, as well as
NCBI's GenBank, for making these genomes available for public
use. We'd also like to acknowledge Hiram Clawson, Chin Li, and
our hard-working QA team for putting together these browsers.
15 May 2012 - New Fugu (fr3)
Assembly Now Available in the Genome Browser:
We are pleased to announce the release of a Genome Browser
for the October 2011 assembly of the Fugu, Takifugu rubripes
(JGI v5.0, UCSC version fr3).
Read more.
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