To receive announcements of new genome
assembly releases, new software features, updates and
training seminars by email, subscribe to the
genome-announce mailing list.
3 January 2012 - Roadmap
Epigenomics Now Available through Data Hub at Washington
We are pleased to announce the release of the Roadmap
Epigenomics data on the UCSC Genome Browser through our
Data Hub function. The Roadmap Epigenomics Project is part
of The NIH Common Fund's Epigenomics Program.
It was launched with the goal of producing a public resource
of human epigenomic data to catalyze basic biology
and disease-oriented research. The Consortium leverages
experimental pipelines built around next-generation sequencing
technologies to map DNA methylation, histone modifications,
chromatin accessibility and small RNA transcripts in stem
cells and primary ex vivo tissues selected to represent the
normal counterparts of tissues and organ systems frequently
involved in human disease. The Consortium expects to deliver
a collection of normal epigenomes that will provide a framework
or reference for comparison and integration within a broad
array of future studies.
All data were produced and processed by the
Roadmap Epigenomics Mapping Consortium, and will be periodically
updated. Genome Browser tracks were constructed and hosted by
VizHub at Washington University in St. Louis.
Tracks are available at UCSC Genome Browser via the Data Hub
function, or follow this
The Roadmap Epigenomics Mapping Consortium is responsible for
the quality of the data.
19 December 2011 - Variant
Call Format (VCF) Now Supported in Genome Browser
We are pleased to announce that the UCSC Genome Browser
now supports Variant Call Format (VCF). VCF is a flexible
and extendable line-oriented text format developed by the
1000 Genomes Project for releases of single nucleotide variants,
indels, copy number variants and structural variants discovered
by the project. Similar to bigBed, bigWig and BAM, the Browser
transfers only the portions of VCF files necessary to display
viewed regions, making VCF a fast and attractive option for
large data sets. VCF files will need to be compressed and
indexed using the tabix package available from
SAMtools. This new format is available
for use in custom tracks and data hubs. For more information
about VCF and tabix, please see our VCF Track Format help page.
7 November 2011 - UMD Cow
Assembly Now Available in Genome Browser
In response to the many requests from the bovine research
community, we now offer the University of Maryland (UMD)
Bos taurus assembly in the Genome Browser, in
addition to the assemblies produced by the Baylor College
of Medicine Human Genome Sequencing Center. The UMD v3.1
assembly (Nov. 2009, UCSC bosTau6) was produced by the
for Bioinformatics and Computational
Biology (CBCB) in College Park, MD.
The UMD 3.1 assembly is based on reads downloaded from
the NCBI Trace Archive, most of which were sequenced by
the Baylor College of Medicine. UMD reports that they were
able to apply several assembly improvement techniques
to produce an assembly that is substantially more accurate
and complete than previous alternative versions, as
evaluated using independent metrics. Based on UMD
statistics, this assembly provides more genome coverage,
closes thousands of gaps, corrects many erroneous
inversions, deletions, and translocations, and fixes
thousands of single-nucleotide errors. For more information,
see Zimin AV et al,
A whole-genome assembly of the domestic
cow, Bos taurus, Genome Biol. 2009;10(4) and
the UMD CBCB
Bos taurus assembly web page.
Downloads of the UMD bovine data and annotations may be
obtained from the UCSC Genome Browser
or Downloads page.
We'd like to thank the UMD CBCB for providing this genome
assembly. The UMD Cow Genome Browser and annotation tracks
were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg
Roe, Steve Heitner, and Donna Karolchik. See the
page for a detailed list of the organizations and
individuals who contributed to this release.
10 October 2011 - Updated Yeast Browser Released:
We are happy to announce the release of an updated browser
for the Saccharomyces cerevisiae yeast genome.
8 September 2011 -
New Navigation and Display Features:
We've added several new features to the Genome Browser
that make it easier to quickly configure and navigate
around in the browser's annotation tracks window.
18 August 2011 -
New Feature: Track Data Hubs:
We are pleased to announce a new feature in the UCSC Genome
Browser: Track Data Hubs. Track hubs are web-accessible
directories of genomic data that can be viewed on the UCSC
Genome Browser alongside native annotation tracks.
==> News Archives