9531fa7cf8d580673e0f0741c033e83c6a10d519 luvina Tue Mar 5 14:57:02 2013 -0800 added dbSNP 137 mm10 announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 59fb118..4908eb1 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,96 +1,101 @@ <!--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 --> <p> - <font face="courier" size="3"><b>11 February 2013 - - Denisova tracks released on hg19 browser</b></font> + <font face="courier" size="3"><b>05 March 2013 + - dbSNP 137 Available for mm10</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> + We are pleased to announce the release of three tracks derived + from dbSNP build 137, available on the mouse assembly (GRCm38/mm10). + dbSNP build 137 is available at NCBI. The new tracks contain + additional annotation data not included in previous dbSNP tracks, + with corresponding coloring and filtering options in the Genome + Browser. </p> <p> - Two supporting datasets and one analysis dataset are now available in the Genome Browser: + As for dbSNP build 137, there are three tracks in this release. + One is a track containing all mappings of reference SNPs to the + mouse assembly, labeled "All SNPs (137)". The other two tracks + are subsets of this track and show interesting and easily defined + subsets of dbSNP: </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). + <li>Common SNPs (137): uniquely mapped variants that appear in + at least 1% of the population + <li>Mult. SNPs (137): variants that have been mapped to more + than one genomic location </ul> <p> - 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. + By default, only the Common SNPs (137) are visible; other + tracks must be made visible using the track controls. + </p> + <p> + You will find the three SNPs (137) tracks on the Mouse Dec. + 2011 (GRCm38/mm10) browser in the "Variation and Repeats" group. + </p> + The tracks were produced at UCSC by Angie Hinrichs and Luvina Guruvadoo. </p> <hr> + + <p> + <font face="courier" size="3"><b>11 February 2013 - + Denisova tracks released on hg19 browser</b></font> + 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. + <a href="goldenPath/newsarch.html#021113">Read more</a>. + </p> + <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>