5c15a81179ba05e7d7dfe2c7809389ed6d755424 donnak Tue Mar 1 10:39:08 2011 -0800 Added news item about panTro3, archived some other items. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 13f70a4..b1cec01 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,142 +1,111 @@ <!--News Section-----------------------------------------------> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="#fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0> <TR><TD> <!--cheap trick to get background on row to be continuous--> <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TD ALIGN="left"> <FONT SIZE="4"><A NAME="TOC"></A><B> News</B></FONT></TD> <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A> </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> + <FONT FACE="courier" SIZE="3"><B>1 March 2011 - +Updated Chimpanzee Browser Released</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> + We are happy to announce the release of a Genome Browser for + the latest release of the chimpanzee (Pan troglodytes) + genome. The Oct. 2010 assembly -- CGSC v2.1.3, + UCSC version panTro3 -- was produced by the + <A HREF="http://genome.wustl.edu/genome.cgi?GENOME=Pan%20troglodytes&SECTION=collaborators" + TARGET=_BLANK>Chimpanzee Sequencing and Analysis + Consortium</A>.</P> <P> - The Zv9 assembly comprises a sequence length of 1.4 Gb in - 26 chromosomes and 1,107 scaffolds. 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>. + This assembly covers about 97 percent of the genome and is + based on 6X sequence coverage. It comprises 192,898 contigs + with an N50 length of 44 kb and 33,990 supercontigs with an + N50 length of 8.4 Mb. + Improvements introduced with the 2.1.3 assembly include the + addition of over 300,000 finishing reads and the merging in + of 640 finished BACS. Approximately 49,000 additional merges + were made in this assembly as compared with the 2.1 + assembly. + <P> + The whole genome shotgun data were derived primarily from + the donor Clint, a captive-born male chimpanzee from the + Yerkes Primate Research Center in Atlanta, GA, USA. + The sequence data were assembled and organized by the + Washington University Genome Center. The underlying whole + genome shotgun data were generated at the Washington + University School of Medicine and the Broad Institute. + For detailed information about the assembly + process, see the sequencing and analysis discussion in the + <A HREF="http://www.ncbi.nlm.nih.gov/nuccore/AACZ00000000" + TARGET=_blank>GenBank accession record</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 Sanger Institute - <A HREF="http://www.sanger.ac.uk/legal/" - TARGET=_blank>guidelines</A> for using these data. + Bulk downloads of the sequence and annotation data are + available via the Genome Browser + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/">FTP + server</A> or the + <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#chimp">Downloads</A> + page. The complete set of sequence reads is available at the + + <A HREF="http://www.ncbi.nlm.nih.gov/Traces" + TARGET=_blank>NCBI trace archive</A>. These data have + <A HREF="goldenPath/credits.html#chimp_use">specific + conditions for use</A>.</P> <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="goldenPath/credits.html#zebrafish_credits">credits</A> - page for a detailed list of the organizations and - individuals who contributed to this release.</P> + We'd like to thank the International Chimpanzee + Sequencing and Analysis Consortium, Washington + University at St. Louis School of Medicine Genome Sequencing + Center, and the Broad Institute for providing this assembly. + We'd also like to acknowledge the UCSC team who worked on + this release: Hiram Clawson, Greg Roe, and Donna Karolchik. + The chimpanzee browser annotation tracks were generated by + UCSC and collaborators worldwide. </P> <P> <HR> - <FONT FACE="courier" SIZE="3"><B>10 January 2011 - Introducing Genome Browser Right-click Navigation</B></FONT> + <FONT FACE="courier" SIZE="3"><B>19 January 2011 - +Browser Released for Zebrafish Zv9 Assembly: </B></FONT> + The most recent zebrafish assembly -- Zv9 (UCSC version + danRer7, Jul. 2010) -- is now available in the UCSC + Genome Browser. + <A HREF="goldenPath/newsarch.html#011911">Read more</A>. <P> + <FONT FACE="courier" SIZE="3"><B>10 January 2011 - Introducing Genome Browser Right-click Navigation: </B></FONT> 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 - generate a high-quality annotation tracks image suitable - for printing.) - <BR><BR> - <img style="border: 2px solid black; margin-left:auto; - margin-right:auto; display: block;" - src="/images/rightclick.png" - alt="Right-click screenshot"> - <BR> + and selecting an option from the displayed menu. + <A HREF="goldenPath/newsarch.html#011011">Read more</A>. <P> - To use the right-click feature, make sure the "Enable - advanced javascript features" option on the - <A -HREF="../cgi-bin/hgTracks?hgTracksConfigPage=configure+tracks+and+display">tracks - configuration page</A> is checked, and configure your - internet browser to allow the display of popup windows from - <em>genome.ucsc.edu</em>. When enabled, the right-click - navigation feature replaces the default contextual menu - typically displayed by your internet browser when you - right-click on the tracks image. A few combinations of the - Mozilla Firefox browser on Mac OS do not support the - right-click menu functionality using secondary click; in - these instances, you must use the explicit ctrl-click action - to display the menu. - <P> - Credit goes to Larry Meyer and Brooke Rhead for doing the - lion's share of the design, development and testing of this - feature, with engineering support from Tim Dreszer and - additional testing by several others on the QA team. - <HR> <FONT FACE="courier" SIZE="3"><B>2 December 2010 - Searching for Tracks Just Got Easier!</B></FONT> - <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>. + <A HREF="goldenPath/newsarch.html#120210">Read more</A>. </P> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>