1d58a54a7f6539f1b77db01b0e505a72ae1f6ee4 donnak Wed Nov 16 08:15:56 2011 -0800 Added UMD cow announcement, archived some news items, fixed some typos etc. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8537181..4610bef 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,141 +1,109 @@
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- - - + 7 November 2011 - UMD Cow + Assembly Now Available in Genome Browser

- 10 October 2011 - Updated Yeast Browser Released -

We are happy to announce an updated Yeast Genome Browser for - Saccharomyces cerevisiae, sacCer3. The April 2011 Saccharomyces cerevisiae - genome assembly (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome - Database (GCA_000146055.2)) was produced by the Saccharomyces Genome Database (SGD™) project.

- + In response to the many requests from the bovine research + community, we now offer the University of Maryland (UMD) + Bos taurus assembly in the Genome Browser, in + addition to the assemblies produced by the Baylor College + of Medicine Human Genome Sequencing Center. The UMD v3.1 + assembly (Nov. 2009, UCSC bosTau6) was produced by the + UMD Center + for Bioinformatics and Computational + Biology (CBCB) in College Park, MD.

+

+ The UMD 3.1 assembly is based on reads downloaded from + the NCBI Trace Archive, most of which were sequenced by + the Baylor College of Medicine. UMD reports that they were + able to apply several assembly improvement techniques + to produce an assembly that is substantially more accurate + and complete than alternative versions, as evaluated using + independent metrics. Based on UMD statistics, this + assembly provides more genome coverage, closes + thousands of gaps, corrects many erroneous inversions, + deletions, and translocations, and fixes thousands of + single-nucleotide errors. For more information, see + Zimina AV et al, + A whole-genome assembly of the domestic + cow, Bos taurus, Genome Biol.2009;10(4) and + the UMD CBCB + Bos taurus assembly web page.

- Chromosomes available in this assembly: chrI, chrII, chrIII, chrIV ... etc ... chrXVI, - and chrM. See also: SGD™ genome snapshot/overview. + Downloads of the UMD bovine data and annotations may be + obtained from the UCSC Genome Browser + FTP server + or Downloads page.

-

- Downloads of the yeast data and annotations may be obtained from the UCSC - Genome Browser FTP server or - Downloads page. - The S. cerevisiae annotation tracks were generated by - UCSC and collaborators worldwide. - -

- We'd like to thank the Saccharomyces Genome - Database (SGD™). The S. cerevisiae Genome Browser and annotation tracks were produced by - Hiram Clawson, Greg Roe, and Steve Heitner. See the Credits page for a detailed list of the organizations and individuals who - contributed to this release. -

- + We'd like to thank the UMD CBCB for providing this genome + assembly. The UMD Cow Genome Browser and annotation tracks + were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg + Roe, Steve Heitner, and Donna Karolchik. See the + Credits + page for a detailed list of the organizations and + individuals who contributed to this release.

+

- - - + + + 10 October 2011 - Updated Yeast Browser Released: + We are happy to announce the release of an updated browser + for the Saccharomyces cerevisiae yeast genome. + Read more. +

8 September 2011 - -New Navigation and Display Features -

+New Navigation and Display Features: We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. -

- Automatic image resizing: The first time the annotation - track window is displayed, or after the Genome Browser has - been reset, the size of the track window is now set by - default to the width that best fits your Internet browser - window. If you subsequently resize your browser window, - you can automatically adjust the annotation track image - size to the new width by clicking the resize button - under the track image. The default width can still be - manually overridden on the Track Configuration page. -

- Scrolling left or right in the track window: You can now - scroll (pan) horizontally through the tracks image by clicking - on the image, dragging the cursor to the left or right, - then releasing the mouse button. The view may be scrolled - by up to one image width. -

- Improved drag-zoom navigation: The browser's - "drag-and-zoom" feature lets you quickly zoom to a - specific region of interest on the annotation tracks image. - To define the region you wish to zoom to, depress the shift - key, click-and-hold - the mouse button on one edge of the desired zoom area - (which can be anywhere in the tracks window), - drag the mouse right or left to highlight the - selection area, then release the mouse button. - The annotation tracks image will automatically zoom to - the new region. The Genome Browser still supports the - earlier implementation of this feature, which restricted - the click-drag to the Base Position track area of the image, - but did not require the shift key to be pressed. -

- Reordering groups of tracks: - You can now vertically reposition an entire group of - associated tracks in the tracks image (such as all the - displayed subtracks in a composite track) by clicking and - holding the gray bar to the left of the tracks, - dragging the group to the new position, then releasing - the mouse button. To move a single track up or down, click - and hold the mouse button on the side label, drag the - highlighted track to the new position, then release the - mouse button. -

- If you haven't yet tried the browser's right-click - menu for quick access to frequently used track - configuration features and functionality, read more - here. -

+ Read more.

18 August 2011 - New Feature: Track Data Hubs: - We are pleased to announce a new feature in the UCSC Genome Browser: Track Data Hubs. Track hubs are web-accessible directories of genomic data - that can be viewed on the UCSC Genome Browser alongside native annotation - tracks. + We are pleased to announce a new feature in the UCSC Genome + Browser: Track Data Hubs. Track hubs are web-accessible + directories of genomic data that can be viewed on the UCSC + Genome Browser alongside native annotation tracks. Read more.

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