5ccd51414ab1c9cb5a643739583b315c9a6b00be
rhead
  Mon Apr 18 15:53:00 2011 -0700
Changed location of link to dbSNP.
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                           <FONT SIZE="4"><A NAME="TOC"></A><B>&nbsp; News</B></FONT></TD>
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                         SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A>
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                     <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
+                    <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
                     &quot;All SNPs (132)&quot;.  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 &quot;clinically associated&quot;</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 &quot;Variation and Repeats&quot; 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>
 		    
 		    <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>
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