90aae127020bbc1565bb62626d030cfac2bd83b4 rhead Mon Apr 18 16:14:11 2011 -0700 On SNP 132 description, changed single -> multiple, and standardized punctuation on PAR. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 108a12f..70a8ca5 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,176 +1,176 @@ <!--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 --> <!-- hg19 snp132 release --> <P> <FONT FACE="courier" SIZE="3"><B>18 April 2011 - dbSNP 132 Available for hg19</B></FONT> </P> <P> We are pleased to announce the release of four tracks derived from <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target=_blank>dbSNP</a> build 132, available on the human assembly (GRCh37/hg19). dbSNP build 132 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> As for prior builds of dbSNP, there is a track that contains all mappings of reference SNPs to the human assembly; it is now labeled "All SNPs (132)". Three new tracks have been added to show interesting and easily defined subsets of dbSNP: </P> <ul> <li> Common SNPs (132): uniquely mapped variants that appear in at least 1% of the population</li> <li>Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated"</li> <li>Mult. SNPs (132): variants that have been mapped to more than one genomic location</li> </ul> <P> By default, only the Common SNPs (132) are visible; other tracks must be made visible using the track controls. </P> <P> The counts of distinct reference SNPs and their mappings to hg19 differ greatly among the tracks: </P> <table border="1" cellpadding="3"> <tr> <th>Track</th> <th>Reference SNPs</th> <th>Mappings to hg19</th> </tr> <tr> <td>Common SNPs (132)</td> <td>13,842,381</td> <td>14,024,295 *</td> </tr> <tr> <td>Flagged SNPs (132)</td> <td>17,899</td> <td>18,084 *</td> </tr> <tr> <td>Mult. SNPs (132)</td> <td>1,114,599</td> <td>3,568,988</td> </tr> <tr> <td>All SNPs (132)</td> <td>30,030,754</td> <td>33,026,121</td> </tr> </table> <P> - * There are more mappings than SNPs even for the Common and Flagged - subsets, because single mappings to alternate haplotype sequences - and the Pseudo-Autosomal Regions on X and Y don't disqualify a SNP + * There are more mappings than SNPs for the Common and Flagged + subsets because multiple mappings to alternate haplotype sequences + or the pseudoautosomal regions on X and Y don't disqualify a SNP from consideration as uniquely mapped. </P> <P> You will find the four SNPs (132) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group. </P> <P> Many thanks to dbSNP at NCBI for the data, and to <a href="http://www.gs.washington.edu/faculty/king.htm" target=_blank>Mary-Claire King</a> at the University of Washington for helpful comments that motivated us to enhance our dbSNP annotations. The tracks were produced at UCSC by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent. </P> <HR> <!-- SHEEP BROWSER RELEASE --> <p> <font face="courier" size="3"><b>18 April 2011 - Sheep Browser Released</b></font> </p> <p>We are happy to announce a Genome Browser for the initial release of sheep (<em>Ovis aries</em>) genome. The Feb. 2010 <em>Ovis aries</em> draft assembly (NCBI project <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10709" target=_blank>10709</a>, <a href="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Ovis_aries/ Ovis_aries_1.0/" target=_blank>GCA_000005525.1</a>) was produced by the <a href="http://www.sheephapmap.org/" target=_blank>International Sheep Genomics Consortium (ISGC) sequencing center</a>. The mitochondrial genome was sequenced by <a href="http://www.uni-giessen.de/cms/" target=_blank>Justus-Liebig-University</a>.</p> <p>There are 27 chromosomes: chr1 - chr26, chrX, plus the mitochondrial sequence chrM from genbank accession NC_001941, for a total sequence length of 2,860,512,983 bases. There are 1,659,241,706 'N' bases in gaps, leaving 1,201,271,277 ACGT bases.</p> <p>The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep genome.</p> <p>We'd like to thank the International Sheep Genomics Consortium (ISGC) sequencing center and Justus-Liebig-University for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Chin Li, Greg Roe, and Luvina Guruvadoo. The sheep browser annotation tracks were generated by UCSC and collaborators worldwide.</p> <hr> <p><FONT FACE="courier" SIZE="3"><B>04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: </B></FONT> Consensus was reached on color standards to represent CNV loss (red) and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA during the 1st annual ISCA Scientific Conference. <A HREF="goldenPath/newsarch.html#030411">Read more</A> </p> <p><FONT FACE="courier" SIZE="3"><B>01 March 2011 - Updated Chimpanzee Browser Released: </B></FONT> We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (<em>Pan troglodytes</em>) genome. <A HREF="goldenPath/newsarch.html#030111">Read more</A> </p> <p><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> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>