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22 January 2014 -
All the DNA on the internet now at your fingertips!
We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser. This
track, produced in collaboration with Microsoft Research, contains the results of a 30-day scan for
DNA sequences from over 40 billion different webpages. The sequences were then mapped with Blat to
the human genome (hg19) and numerous other species including mouse (mm9), rat (rn4), and zebrafish
(danRer7). The data were extracted from a variety of sources including patents, online textbooks,
help forums, and any other webpages that contain DNA sequence. In essence, this track displays the
Blat alignments of nearly every DNA sequence on the internet! The
track description page contains more details on how the track was generated.
We would like to acknowledge Max Haeussler and Matt Speir from the UCSC Genome Browser staff
and Bob Davidson from Microsoft Research for their hard work in creating this track.
14 January 2014 -
Two E. coli comparative assembly hubs now available
We're pleased to add two new assembly hubs produced by the UCSC
David Haussler lab
to our collection of publicly available hubs. The new hubs feature over 60 bacterial assemblies,
including more than 55 different E. coli strains. The assembly annotations include genes, pathogenic
genes, conservation, GC percent, repetitive elements and much more.
These hubs focus on comparative genomics and showcase the new "snake" track type. Snakes, which
visualize alignments from
(HAL) files, provide a way to view sets of pairwise gapless alignments that may overlap on both
the chosen genome (reference) and the query genome, and show various types of genomic variations
such as insertions, substitutions, and duplications. More details about the new snake track display
and its configuration options can be found on our Genome Browser
To access and view these hubs, navigate to the
Track Hub gateway page
and select one of the two E. coli comparative assembly hubs from the Public Hubs list.
We would like to acknowledge Ngan Nguyen, Glenn Hickey, Brian Raney, Joel Armstrong, Benedict Paten,
Matt Speir, and Luvina Guruvadoo for their hard work in creating these hubs.
27 November 2013 -
100 Species Conservation Track now available on hg19
We're happy to announce the release of a new track on the hg19/GRCh37 human Genome Browser.
The new Conservation track shows multiple alignments of 100 species and measurements of
evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package.