8058149ada1f2b5c5be9822ef0c4095af1834ff2 pauline Mon Feb 11 15:41:11 2013 -0800 Adding entry for Denisova tracks. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 69d1bed..4a626b0 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,79 +1,96 @@ <!--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="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> - - <font face="courier" size="3"><b>25 January 2013 - - Southern White Rhinoceros Genome Browser Released</b></font> <p> - A Genome Browser is now available for the Southern White Rhinoceros - (<em>Ceratotherium simum simum</em>) assembly released by the Broad - Institute in May 2012 (Broad version cerSimSim1.0, UCSC version cerSim1). This - genome was sequenced and assembled at the Broad Institute using samples - provided by Dr. Oliver Ryder at the San Diego Zoo Institute for Conservation - Research. For more information and statistics about this assembly, - see the NCBI assembly record for - <a href="http://www.ncbi.nlm.nih.gov/assembly/406328/" - target="_blank">CerSimSim1.0</a>. + <font face="courier" size="3"><b>11 February 2013 - + Denisova tracks released on hg19 browser</b></font> + <br> + In conjunction with the publication of the paper by Meyer <em>et al.</em> + <a href="http://www.ncbi.nlm.nih.gov/pubmed/22936568"> + A High-Coverage Genome Sequence from an Archaic Denisovan Individual</a> + the UCSC Genome Browser is hosting a set of new tracks. Briefly, Meyer <em>et al.</em> + applied a novel single-stranded DNA library preparation method to DNA previously + extracted from 40mg of a phalanx bone excavated from Denisova Cave in the + Altai Mountains in southern Siberia. + </p> + <p> + Two supporting datasets and one analysis dataset are now available in the Genome Browser: + </p> + <ul> + <li>Modern Human Variants : variant calls made from sequence reads of eleven individuals + mapped to the human genome, used in statistical analyses to put the divergence of the + Denisova genome into perspective with regard to present-day humans. + <li>Denisova Sequence: high-coverage (30X) sequence reads from an archaic Denisovan + individual mapped to the human genome reference assembly. + <li>Modern Human Derived, Denisova Ancestral: mutations in the modern human lineage + that rose to fixation or near fixation since the split from the last common + ancestor with Denisovans, along with predicted functional effects from Ensembl's + Variant Effect Predictor (VEP). + </ul> <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome - Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/cerSim1/">FTP server</a> - or the - <a href="http://hgdownload.cse.ucsc.edu/downloads.html#white_rhinoceros">Downloads</a> - page. Please observe the - <a href="goldenPath/credits.html#white_rhinoceros_use">conditions for use</a> - when accessing and using these data sets. The annotation tracks for this browser - were generated by UCSC and collaborators worldwide. See the - <a href="goldenPath/credits.html#white_rhinoceros_credits">Credits</a> page for a - detailed list of the organizations and individuals who contributed to this release. + We'd like to thank Richard Green and the many authors of the Science paper + for providing the UCSC Genome Browser with these data. + We'd also like to acknowledge the hard work of the UCSC Genome Browser staff + who pulled together the annotations and information for these tracks: + Angie Hinrichs and Pauline Fujita. </p> <hr> <p> + <font face="courier" size="3"><b>25 January 2013 - + Southern White Rhinoceros Genome Browser Release: </b></font> + We are pleased to announce the release of a Genome Browser for the May 2012 + assembly of the Southern White Rhinoceros, <em>Ceratotherium simum simum</em> + (Broad Institute version cerSimSim1.0, UCSC version cerSim1). + <a href="goldenPath/newsarch.html#012513">Read more</a>. + </p> + + <p> <font face="courier" size="3"><b>22 January 2013 - New Baboon (papAnu2) Assembly Now Available in the Genome Browser: </b></font> We are pleased to announce the release of a Genome Browser for the March 2012 assembly of the Olive Baboon, <em>Papio anubis</em> (Baylor Panu_2.0, UCSC version papAnu2). <a href="goldenPath/newsarch.html#012213">Read more</a>. </p> <p> <font face="courier" size="3"><b>15 January 2013 - New Lamprey (petMar2) Assembly Now Available in the Genome Browser: </b></font> We are pleased to announce the release of a Genome Browser for the September 2010 assembly of the Lamprey, <em>Petromyzon marinus</em> (WUGSC 7.0, UCSC version petMar2). <a href="goldenPath/newsarch.html#011513">Read more</a>. </p> <!-- start archives --> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>