0b514bc156e8d2de88e38d5b42411c27fa7623ec donnak Wed Jan 19 09:39:57 2011 -0800 Added announcement about danRer7 browser. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index c7d3ece..375d8bb 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,30 +14,77 @@ </TD></TR></TABLE> </TD></TR></TABLE> <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> <P> + <FONT FACE="courier" SIZE="3"><B>19 January 2011 - +Browser Released for Zebrafish zv9 Assembly</B></FONT> + <P> + The most recent zebrafish assembly -- zv9 (UCSC version + danRer7, Jul. 2010) -- is now available in the UCSC + Genome Browser. This assembly was produced by + <A HREF="http://www.sanger.ac.uk/" + TARGET=_blank>The Wellcome Trust Sanger Institute</A>, UK. + </P> + <P> + The zv9 assembly comprises a sequence length of 1.4 Gb in + 26 chromosomes and 1,107 scaffolds with a coverage of + 6.5-7x. This assembly is based on a clone path sorted with + the high-density meiotic map SATMAP (Clark et al., in + preparation). The data freeze was taken on 1 April 2010. + The remaining gaps were filled with sequence from WGS31, a + combined Illumina and capillary assembly. The assembly + integration process involved sequence alignemnts as well as + cDNA, marker and BAC/Fosmid end sequence placements. + The zebrafish mitochondrial sequence is also available in + the Genome Browser as the virtual chromosome chrM. For + more details about the zv9 assembly, see the Sanger + Institute page for the + <A HREF="http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml" + TARGET=_blank><em>Danio rerio</em> Sequencing Project</A>. + </P> + + <P> + The danRer7 sequence and annotation data can be + downloaded from the UCSC Genome Browser + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer7/">FTP server</A> + or + <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#zebrafish">downloads</A> + page. Please review the + <A HREF="http://www.sanger.ac.uk/notices/use-policy.shtml" + TARGET=_blank>guidelines</A> for using these data. + <P> + We'd like to thank the Wellcome Trust Sanger Institute + for providing this assembly. + The UCSC zebrafish Genome Browser + was produced by Hiram Clawson, Greg Roe, Mary Goldman, + Brian Raney and Donna Karolchik. See the + <A HREF="credits.html#zebrafish_credits">credits</A> + page for a detailed list of the organizations and + individuals who contributed to this release.</P> + <P> + <HR> <FONT FACE="courier" SIZE="3"><B>10 January 2011 - Introducing Genome Browser Right-click Navigation</B></FONT> <P> Several of the common display and navigation operations offered on the Genome Browser tracks page may now be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed menu. Depending on context, the right-click feature will let you change the track display mode, zoom in or out to the exact position coordinates of the feature, open the "Get DNA" window at the feature's coordinates, display details about the feature, open a popup window to configure the track's display, or display the entire tracks image in a separate window for inclusion in spreadsheets or other documents. (Note that the "PDF/PS" option in the Genome Browser top navigation bar can also be used to @@ -75,31 +122,21 @@ <P> The number of genome assemblies and annotation tracks in the UCSC Genome Browser has increased exponentially over the past few years. Along with this growth, it has become more difficult for browser users to sort through the many tracks to find the data they're interested in. <P> With our latest Genome Browser release, we've introduced a new track search feature that will help you to quickly and easily find and display specific annotation data sets. The search feature is available via the "track search" button on the browser gateway and tracks display pages. <A HREF="goldenPath/newsarch.html#120210">Read more</A>. - <P> - <FONT FACE="courier" SIZE="3"><B>24 August 2010 - New Drag and Reorder Functionality Released </B></FONT> - <P> - It is now possible to rearrange the order that tracks appear - in the browser image directly from the browser image itself. - To reorder tracks, click-and-hold the side label or gray - mini-button of a single track and drag the highlighted track - to a new position within the image. - <A HREF="goldenPath/newsarch.html#082410">Read -more</A>. </P> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>