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22 Apr 2016
- Data from the Lens PatSeq Database Now Available
We are pleased to announce the release of a set of tracks showing the genomic mapping of
biomedical sequences submitted as part of patent application documents worldwide. The sequence
data, mappings and associated patent information were obtained from the
PatSeq database provided by
The Lens. The PatSeq data are
mapped to the genome, and the individual sequence features within the tracks are then
color-coded to indicate their status within the associated patent documents.
Track details pages show information about the patent documents in which the sequences
are referenced, and provide a link to The Lens PatSeq Analyzer tool for the given chromosome
range. The PatSeq data are divided into two tracks: a bulk patent track for sequences affiliated
with patents in which more than 100 sequences were submitted, and a non-bulk patent track
for all other sequences. These tracks are currently present on the human (hg19), mouse (mm10),
and Ebola virus (eboVir3) genomes.
Thanks to our collaborators at The Lens, Osmat Jefferson and Deniz Koellhofer, for providing the
data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of
the UCSC Genome Browser team, for their efforts in creating these tracks.
20 April 2016
- New GTEx Gene Expression Track for hg19 and hg38
We are excited to announce the release of a new gene expression track based on data from the NIH
This track displays tissue-specific gene expression based on RNA-seq in 53 tissues from 570
donors obtained from the GTEx 'midpoint' data release (V6, October 2015).
The original data for this
track can be found at the GTEX Portal
hosted by the Broad Institute.
This track also features a new gene expression display method that extends the traditional Genome
Browser display — a horizontal bar graph. Every gene is annotated by a graph with colored
bars, each of which corresponds to a specific tissue assayed by the GTEx project. Within
a graph, the bar color indicates the tissue type, using GTEx conventions, and the bar height
depicts the median expression level (in RPKM).
To quickly view the tissue and expression level represented by a bar in the tracks display,
mouse over the bar in the graph.
The complete tissue color legend is shown on the
track configuration page,
and can also be popped up for viewing alongside the track using the right-click menu.
Below the bar graph, a line is shown indicating the gene extent that was used to generate the
annotation, colored by gene class using GENCODE conventions
(e.g. blue for protein-coding,
green for non-coding).
User alert: In the figure above, do you notice how the bar graph sometimes extends past the
righthand end of the associated gene annotation? This is because all bar graphs in the
display are the same width (and have the same tissue ordering) to facilitate comparison.
For example, in this figure (which may also be viewed
the three tall bars in the annotation of the TCAP gene indicate that this entire gene is
highly expressed in cardiac and skeletal muscle. It does not indicate that there are
expression peaks in the intergenic region beyond the gene!
Similar to other Genome Browser track displays, clicking on the graph will bring up a description
page that shows a detailed box-and-whiskers plot of
the RPKM data, as well as a description of the methods used to generate the data.
Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of this
15 April 2016 -
dbSNP 146 Available for hg19 and hg38:
We are pleased to announce the release of four tracks derived
from NCBI dbSNP Build 146 data.
15 April 2016
- Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available.