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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
We are excited to announce the release the 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 alleles." Each haplotype allele is a
distinct set of variants found on at least one of the 1000 Genomes
subject chromosomes. For each haplotype, we display its frequency in
the 1000 Genomes populations and indicate the frequency with which it
occurs homozygously in each population. Unexpected frequencies of
occurrence may thus be used to identify alleles that merit further
study. Predicted protein sequence for common haplotypes can also be
displayed, allowing differences among alleles to be used to identify
differences at the amino acid level.
To see the Gene Alleles feature, go to the details page for any
protein-coding gene in the UCSC Genes track and click the "Gene
Alleles" link in the top right cell of the "Page Index" matrix. This
will take you to the "Common Gene Haplotype Alleles" section. For
more information on this feature please see this help doc:
Many thanks to Tim Dreszer, Brooke Rhead and Pauline Fujita for their work on this feature.
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.
The new release has 82,960 total transcripts, compared with
80,922 in the previous version. The total number of canonical
genes has increased from 31,227 to 31,848. Comparing the new
gene set with the previous version:
- 74,657 transcripts did not change between versions.
- 88 transcripts were not carried forward to the new version.
- 5,556 transcripts are "compatible" with those in the previous set,
meaning that the two transcripts show consistent splicing.
In most cases, the old and new transcripts differ in the
lengths of their UTRs.
- 621 transcripts overlap with those in the previous set but
do not show consistent splicing, i.e., they contain overlapping
introns with differing splice sites.
More details about the new UCSC Genes track can be found on
the UCSC Genes track description page.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo
for their work on this track!
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.