0fc56ebaad6baeafd482ef2d7f7bd89a6ab84f46 greg Mon Apr 18 14:11:05 2011 -0700 Changed header html back to old style, as I didn't realize this page was set to html3.2 :P diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 90d2126..20d018b 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,264 +1,264 @@ <!--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 March 2011 - dbSNP 132 Available for hg19</B></FONT> </P> <P> We are pleased to announce the release of four tracks derived from dbSNP build 132, available on the human assembly (GRCh37/hg19). dbSNP build 132 is <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target=_blank>available at NCBI</a>. 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 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 style="font-weight: bold; font-size: 16px; font-family: 'courier', serif"> - 18 March 2011 - Sheep Browser Released + <p> + <font face="courier" size="3"><b>18 March 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> </P> <P> 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. </P> <P> At the recent ISCA Scientific Conference in Atlanta, GA, Nigel Carter, representing DECIPHER, made a plea for a standardized color scheme for representation of CNV loss (deletion) or gain (duplication). Discussions in person and by email with leaders of major CNV/genomic databases (including DGV, dbVar, ISCA, and the UCSC Genome Browser) resulted in the recommendation to utilize red to represent loss/deletion (consistent with the original convention for CGH on metaphase chromosomes) and blue to represent gain/duplication (avoiding green which is difficult for color-blind individuals to discriminate from red). </P> <P> Announcement reprinted from the website for the International Standards for Cytogenomic Arrays (<A HREF = "http://iscaconsortium.org" TARGET = _BLANK>ISCA</A>) Consortium. The UCSC Genome Browser is now conforming to this standard for the DECIPHER track and the DGV track on human assemblies (which was released today) and on any future tracks derived from dbVar. </P> <P> Thanks to Nigel Carter, Steve Scherer, Deanna Church, Angie Hinrichs, Fan Hsu, Pauline Fujita and Robert Kuhn. </P> <HR> <P> <FONT FACE="courier" SIZE="3"><B>01 March 2011 - Updated Chimpanzee Browser Released</B></FONT></P> <P> We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (<em>Pan troglodytes</em>) 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> 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> 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 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>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. <A HREF="goldenPath/newsarch.html#011011">Read more</A>. <P> <FONT FACE="courier" SIZE="3"><B>2 December 2010 - Searching for Tracks Just Got Easier! </B></FONT> </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>. </P> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>