74410bb3b2efa09a970d0fccdd645f52573bf396 ann Fri Dec 11 11:04:12 2015 -0800 holiday greetings. thanks Brian Lee! diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index ada4821..619c394 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,138 +1,145 @@
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9 December 2015 — Data from 1000 Genomes Project Phase 3 Now Available

We have made data from Phase 3 of the 1000 Genomes Project available for the hg19 version of the human assembly. The data includes almost 90 million variants in the form of single nucleotide variants (SNVs), insertions/deletions (InDels), and structural variants (SVs). Each variant includes a detail page that incorporates links to the variant in the dbSNP database, quality scores, and allele frequency information for various populations. More information is available on the track description page.

In addition to variant calls, the data includes two tracks that highlight regions of the genome that are accessible to next generation sequencing technologies that utilize paired-end reads. One track contains regions that meet the 1000 Genomes Project "pilot" criteria while the other contains regions that meet a more "strict" set of guidelines. More information about how these accessible regions were identified can be found on the track description page.

Thank you to the 1000 Genomes Project and Tom Blackwell and Mary Kate Wing at the University of Michigan for making these data available. Thank you to Angie Hinrichs and Matthew Speir at UCSC for their work on these tracks.

25 November 2015 — New "View - In External Tools" Menu Sends Data to Prediction Websites!

Do you often get the current sequence with "View - DNA" just to copy and paste it into another website? With the new menu "View - In External Tools" you can now send the current region to remote tools with two clicks.

For example, when browsing hg38 and zoomed in on the start of a gene like ABO at chr9:133,255,000-133,255,555, click the View menu and select "In External Tools", or simply type the keyboard shortcut "s" then "t", to send the region to a list of different prediction tools.

Some of the available tools (not available for all assemblies or all zoom levels) are primer design and restriction enzyme predictions (Primer3Plus, Primer-BLAST, NEBCutter), mRNA and protein predictions (RegRNA 2, Riboswitches, RNAfold, PFAM), cis-regulatory predictions (Promoter 2, RSAT Metazoa), and CRISPR/Cas9 predictions (CRISPOR, CHOPCHOP), as well as links to view the region at NCBI or Ensembl. You can suggest other tools via our Suggestion Box.

Credit goes to Max Haeussler for implementing this new feature.

3 November 2015 — New quick links for the Genome Browser's top menu bar : The "Genomes" menu now features direct links to jump to browsing the human (hg38 and hg19) and mouse (mm10 and mm9) assemblies! Read more.

23 September 2015 — New keyboard shortcuts on the Genome Browser : It's now possible to zoom in and out, navigate left and right, hide all tracks, configure the browser display and much more using only your keyboard. Use the "?" key to view the entire list of shortcuts. Read more.