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blog for posts about Genome Browser tools, features, projects and more.
12 August 2015 —
New blog post: How to share your UCSC screenthoughts
Do you want to save your UCSC Browser screenthoughts, or share them with a colleague,
or make a slide for a talk, or publish them in a paper? Saving the state of your screen
can take two forms: static or dynamic. You can snap and save a picture of the screen,
or you can share a link to an active Genome Browser. We talk about both approaches
and discuss some of the advantages and pitfalls of each.
29 June 2015 —
GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly
In a move towards standardizing on a common gene set within the bioinformatics
community, UCSC has made the decision to adopt the GENCODE set of gene models
as our default gene set on the human genome assembly. Today we have released
the GENCODE v22 comprehensive gene set as our default gene set on human
genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set
generated by UCSC. To facilitate this transition, the new gene set employs
the same familiar UCSC Genes schema, using nearly all the same table names
and fields that have appeared in earlier versions of the UCSC set.
By default, the browser displays only the transcripts tagged as "basic" by the
GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in
the Genes and Gene Predictions track group. However, all the transcripts in the
GENCODE comprehensive set are present in the tables, and may be viewed by
adjusting the track configuration settings for the All GENCODE super-track.
The most recent version of the UCSC-generated genes can still be accessed in
the track "Old UCSC Genes".
The new release has 195,178 total transcripts, compared with 104,178 in the
previous version. The total number of canonical genes has increased from
48,424 to 49,534. Comparing the new gene set with the previous version:
- 9,459 transcripts did not change.
- 22,088 transcripts were not carried forward to the new version.
- 43,681 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.
- 28,950 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 GENCODE Basic track can be found on the
GENCODE Basic track description page.
26 June 2015 —
New Bonobo (panPan1) Assembly Now Available in the Genome Browser:
We are pleased to announce the release of a Genome Browser for the May 2012
assembly of bonobo, Pan paniscus (Max-Planck Institute panpan1, UCSC
12 June 2015 —
Have you ever wished that the Table Browser could associate your custom track items
with some other track, while retaining the item names from both? We have released a
new tool that can do just that, and more: the Data Integrator.