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22 July 2013
- Variant Annotation Integrator
In order to assist researchers in annotating and prioritizing thousands
of variant calls from sequencing projects, we have developed the Variant
Annotation Integrator (VAI). Given a set of variants uploaded as a
custom track (in either pgSnp
or VCF format), the VAI will
return the predicted functional effect (e.g., synonymous, missense,
frameshift, intronic) for each variant. The VAI can optionally add
several other types of relevant information, including: the
identifier if the variant is found in dbSNP, protein damage scores for
missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP),
and conservation scores computed from multi-species alignments. The VAI
also offers filters to help narrow down results to the most interesting
Future releases of the VAI will include more input/upload options,
output formats, and annotation options, and a way to add information
from any track in the Genome Browser, including custom tracks.
There are two ways to navigate to the VAI: (1) From the "Tools"
menu, follow the "Variant Annotation Integrator" link. (2)
After uploading a custom track, hit the "go to variant annotation
integrator" button. The user's guide is at the bottom of the page,
under "Using the Variant Annotation Integrator."
Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and
Jonathan Casper for their input and work on this feature.
2 July 2013
- Assembly Data Hubs
We are pleased to announce a new feature in the UCSC Genome Browser:
Assembly Data Hubs.
Assembly Data Hubs extend the functionality of Track Data Hubs to
assemblies that are not hosted natively on the Browser. Assembly Data
Hubs were developed to address the increasing need for researchers to
annotate sequence for which UCSC does not provide an annotation
database. They allow researchers to include the underlying reference
sequence, as well as data tracks that annotate that sequence. Sequence
is stored in the UCSC twoBit format, and the annotation tracks are
stored in the same manner as Track Data Hubs.
To read more about using Assembly Data Hubs, or about creating your
own, please see these guides:
Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature.
2 July 2013
- New Gene Alleles feature on the details pages of UCSC genes:
For each protein-coding gene in the UCSC Genes track, variant data from
the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000
Genomes Project have been distilled into "gene haplotype
28 June 2013
- New UCSC Genes Track Released for GRCh37/hg19: We're happy
to announce the release of an updated UCSC Genes track for the
GRCh37/hg19 human Genome Browser.
27 June 2013
- New Official European Mirror Released: Announcing
an official mirror for European users, with automatic
26 June 2013
- Suggestion Box Released:
Due to popular demand, we have created a suggestion box for track, assembly,
tool, and other feature requests.