cb72f93299e06e1f3061575037ae21a58f8cd892 donnak Wed Nov 23 01:49:44 2011 -0800 Made a few more edits to cow announcement, fixed a few format glitches and typos, including some noted by Steve. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 4610bef..7139746 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,109 +1,110 @@ <!--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><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></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 --> <FONT FACE="courier" SIZE="3"><B>7 November 2011 - UMD Cow Assembly Now Available in Genome Browser</B></FONT> <P> In response to the many requests from the bovine research community, we now offer the University of Maryland (UMD) <em>Bos taurus</em> 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 <A HREF="http://www.cbcb.umd.edu/" TARGET=_blank>UMD Center for Bioinformatics and Computational Biology</A> (CBCB) in College Park, MD. </P> <P> 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 <em>et al</em>, + and complete than previous 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 Zimin AV <em>et al</em>, <A HREF="http://genomebiology.com/2009/10/4/R42" TARGET=_blank>A whole-genome assembly of the domestic - cow, Bos taurus</A>, <em>Genome Biol.</em>2009;10(4) and + cow, <em>Bos taurus</em></A>, <em>Genome Biol.</em> 2009;10(4) and the UMD CBCB - <A HREF="http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml">Bos taurus assembly</A> web page.</P> + <A HREF="http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml" + TARGET=_blank><em>Bos taurus</em> assembly</A> web page.</P> <P> Downloads of the UMD bovine data and annotations may be obtained from the UCSC Genome Browser <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/">FTP server</A> or <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#cow">Downloads</A> page. </P> <P> 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 <A HREF="goldenPath/credits.html#cow_credits">Credits</A> page for a detailed list of the organizations and individuals who contributed to this release. </P> <P> <HR> <!-- start archives --> <!-- sacCer3 Assembly Release --> <FONT FACE="courier" SIZE="3"><B>10 October 2011 - Updated Yeast Browser Released: </B></FONT> We are happy to announce the release of an updated browser for the <em>Saccharomyces cerevisiae</em> yeast genome. <A HREF="goldenPath/newsarch.html#101011">Read more</A>. </P> <!-- New javascript features --> <P> <FONT FACE="courier" SIZE="3"><B>8 September 2011 - New Navigation and Display Features: </B></FONT> 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. <A HREF="goldenPath/newsarch.html#090811">Read more</A>. <!-- data hubs release --> <P> <FONT FACE="courier" SIZE="3"><B>18 August 2011 - New Feature: Track Data Hubs: </B></FONT> 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. <A HREF="goldenPath/newsarch.html#081811">Read more</A>. </P> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>