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-- - 6 May 2016 - - New Gateway Coming 5/10/16! -
- The UCSC Genome Browser team is proud to announce that we will soon release - a newly designed Gateway, which will be live on the public site Tuesday afternoon - (PDT), May 10th, 2016. Another announcement will be shared Tuesday with further - details and a demonstration video.
-- While the main functionality remains unchanged as a gateway to all available genome - browsers, several helpful new features have been added:
-- Here is sneak picture of the new Gateway web page.
-- We hope that you will enjoy the new Gateway page next week! As always, we invite your - questions, comments, and suggestions as directed through the details on our Contact Us web page. -
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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 - Genotype-Tissue Expression - (GTEx) project. - 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). -
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- 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 - here), - 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 - feature. -
+ + 10 May 2016 - New Gateway Page! ++ The UCSC Genome Browser team is proud to announce a newly designed + Gateway web page. + While the main functionality remains unchanged as a gateway to all available + genome browsers on all available genome assemblies, several helpful new + features have been added:
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- Autocomplete search for any genome browser, genome version, or public hub +
- Browse available genome browser species by scrolling through a visual + "tree" menu based on phylogenetic order +
- Quick access shortcuts to popular browsers +
- New style and color scheme +
+ Please see our new UCSC Genome Browser Gateway video + for an introduction to these new features. As we continue to expand our + collection of high-quality, reviewed data by adding more genome assemblies + to our public site, the new autocomplete search functionality provides an + improved method for navigating to genome assemblies. As an alternative to + scrolling through long drop-down menus of genome assembly options, you can + now simply enter assembly search terms for autocomplete recognition, + providing quick access to your genome assembly of interest.
++ Please note the following differences in navigation, which used to appear + as links directly from the previous version of the Gateway web page. New + navigation for the following tools can all be found in the top horizontal + blue menu bar:
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- Browser Reset: "Genome Browser" > "Reset All User Settings" +
- Track Search: "Genome Browser" > "Track Search" +
- Add Custom Tracks: "My Data" > "Custom Tracks" +
- Track Hubs: "My Data" > "Track Hubs" +
- Configure Tracks and Display: "Genome Browser" > "Configure" +
+ We would like to acknowledge the following people for their contributions + to the new Gateway: original art by Jeff West Design, concept by Robert Kuhn, + software design by Angie Hinrichs, and quality assurance by Cath Tyner.
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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 containing data from the Lens PatSeq database in the UCSC Genome Browser. Read more.
19 April 2016 - - New Genotyping Tissue Expression Track for hg19 and hg38! -
+ - New Genotyping Tissue Expression Track for hg19 and hg38!: We are excited to announce the release of a new track based on data from the Genotyping Tissue Expression Consortium V6 data freeze. - Read more. ---> - -
- 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. - Read more. -
- -- 15 April 2016 - - Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available. - Read more. -
+ Read more.