284a175e985cde818c02a65aecb8524be9d9bb2a luvina Mon Jan 21 10:46:04 2013 -0800 added announcement for new baboon assembly papAnu2 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 4031fd2..a75e01c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -13,179 +13,75 @@ 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>22 January 2013 - + New Baboon (papAnu2) Assembly Now Available in the Genome Browser</b></font> + <p> + 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). + The whole genome shotgun assembly was provided by + <a href="https://www.hgsc.bcm.edu/content/baboon-genome-project" + target="_blank">The Baylor College of Medicine Human Genome Sequencing Center</a>. + There are 72,500 scaffolds with a total size of 2,948,380,710 bases. + </p> + + <p> + Bulk downloads of the sequence and annotation data are available via the Genome Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/" target="_blank">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#baboon" target="_blank">Downloads</a> + page. These data have + <a href="/goldenPath/credits.html#baboon_use" target="_blank">specific conditions for use</a>. + The baboon (papAnu2) browser annotation tracks were generated by UCSC and collaborators + worldwide. See the + <a href="/goldenPath/credits.html#baboon_credits" target="_blank">Credits</a> + page for a detailed list of the organizations and individuals who contributed to this release. + </p> + + <hr> + <font face="courier" size="3"><b>15 January 2013 - New Lamprey (petMar2) Assembly Now Available in the Genome Browser</b></font> <p> 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). The whole genome shotgun assembly was provided by <a href="http://genome.wustl.edu/genomes/detail/petromyzon-marinus/" target="_blank">The Genome Institute at Washington University</a>. There are 25,006 scaffolds with a total size of 885,550,958 bases. </p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar2/" target="_blank">FTP server</a> or the <a href="http://hgdownload.cse.ucsc.edu/downloads.html#lamprey" target="_blank">Downloads</a> page. These data have <a href="/goldenPath/credits.html#lamprey_use" target="_blank">specific conditions for use</a>. The lamprey (petMar2) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#lamprey_credits" target="_blank">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> - <hr> - - <font face="courier" size="3"><b>20 December 2012 - - 28 New Vertebrate Assemblies!</b></font> - <p> - Over the past several weeks, we have released 28 new vertebrate assemblies on the - public Genome Browser website, featuring 22 new species and 6 assembly updates. - These assemblies were added to support the 60-species Conservation track on the - latest mouse assembly (mm10/GRCm38). Several of these species were originally - sequenced and assembled for the Mammalian Genome Project (Lindblad-Toh - <em>et al</em>., <em>Nature</em> 2011)*. - <P> - <b><em>Primates:</em></b> - <UL> - <LI> <b>Baboon</b> (<em>Papio hamadryas</em>) <b>papHam1</b> – - Pham_1.0 (Nov. 2008) from the Baylor College of Medicine HGSC - - <LI> <b>Bushbaby</b> (<em>Otolemur garnettii</em>) <b>otoGar3</b> – - OtoGar3 (Mar. 2011) from the Broad Institute - - <LI> <b>Chimpanzee</b> (<em>Pan troglodytes</em>) <b>panTro4</b> – - Build 2.1.4 (Feb. 2011) from the Chimpanzee Genome Sequencing Consortium - <LI> <b>Gibbon</b> (<em>Nomascus leucogenys</em>) <b> nomLeu2</b> – - Nleu1.1 (Jun. 2011) from the Gibbon Genome Sequencing Consortium - - <LI> <b>Mouse lemur</b> (<em>Microcebus murinus</em>) <b>micMur1</b> – - MicMur1.0 (Jul. 2007) from the Broad Institute - - <LI> <b>Rhesus macaque</b> (<em>Macaca mulatta</em>) <b>rheMac3</b> – - CR_1.0 (Oct. 2010) from the Beijing Genomics Institute - - <LI> <b>Squirrel monkey</b> (<em>Saimiri boliviensis</em>) - <b>saiBol1</b> – SaiBol1.0 (Oct. 2011) from the Broad Institute - - <LI> <b>Tarsier</b> (<em>Tarsius syrichta</em>) <b>tarSyr1</b> – - Tarsyr1.0 (Aug. 2008) from WUSTL and the Broad Institute - </UL> - </p> - <p> - <b><em>Other mammals:</em></b> - <UL> - <LI> <b>Alpaca</b> (<em>Vicugna pacos</em>) <b>vicPac1</b> – - VicPac1.0 (Jul. 2008) from the Broad Institute - - <LI> <b>Armadillo</b> (<em>Dasypus novemcinctus</em>) <b>dasNov3</b> – - DasNov3 (Dec. 2011) from the Broad Institute - - <LI> <b>Cat</b> (<em>Felis catus</em>) <b>felCat5</b> – - Felis_catus-6.2 (Sep. 2011) from the International Cat Genome Sequencing Consortium - - <LI> <b>Dolphin</b> (<em>Tursiops truncatus</em>) <b>turTru2</b> – - Ttru_1.4 (Oct. 2011) from the Baylor College of Medicine HGSC - - <LI> <b>Hedgehog</b> (<em>Erinaceus europaeus</em>) <b>eriEur1</b> – - Draft_v1 (Jun. 2006) from the Broad Institute - - <LI> <b>Kangaroo rat</b> (<em>Dipodomys ordii</em>) <b>dipOrd1</b> – - DipOrd1.0 (Jul. 2008) from Baylor College of Medicine HGSC and the Broad Institute - - <LI> <b>Manatee</b> (<em>Trichechus manatus latirostris</em>) <b>triMan1</b> – - TriManLat1.0 (Oct. 2011) from the Broad Institute - - <LI> <b>Megabat</b> (<em>Pteropus vampyrus</em>) <b>pteVam1</b> – - PteVap1.0 (Jul. 2008) from the Broad Institute - - <LI> <b>Naked mole rat</b> (<em>Heterocephalus glaber</em>) <b>hetGla2</b> – - HetGla_female_1.0 (Jan. 2012) from the Broad Institute - - <LI> <b>Pig</b> (<em>Sus scrofa</em>) <b>susScr3</b> – - Sscrofa10.2 (Aug. 2011) from the Swine Genome Sequencing Consortium - - <LI> <b>Pika</b> (<em>Ochotona princeps</em>) <b>ochPri2</b> – - OchPri2 (Jul. 2008) from the Broad Institute - - <LI> <b>Rock hyrax</b> (<em>Procavia capensis</em>) <b>proCap1</b> – - Procap1.0 (Jul. 2008) from the Baylor College of Medicine HGSC - - <LI> <b>Shrew</b> (<em>Sorex araneus</em>) <b>sorAra1</b> – - SorAra1.0 (Jun. 2006) from the Broad Institute - - <LI> <b>Sloth</b> (<em>Choloepus hoffmanni</em>) <b>choHof1</b> – - ChoHof1.0 (Jul. 2008) from the Broad Institute - - <LI> <b>Squirrel</b> (<em>Spermophilus tridecemlineatus</em>) <b>speTri2</b> – - SpeTri2.0 (Nov. 2011) from the Broad Institute - - <LI> <b>Tree shrew</b> (<em>Tupaia belangeri</em>) <b>tupBel1</b> – - Tupbel1.0 (Dec. 2006) from the Broad Institute - </UL> - </p> - <p> - <b><em>Other vertebrates:</em></b> - <UL> - <LI> <B>Atlantic cod</b> (<em>Gadus morhua</em>) <b>gadMor1</b> – - GadMor_May2010 (May 2010) from Genofisk - - <LI> <B>Budgerigar</b> (<em>Melopsittacus undulatus</em>) <b>melUnd1</b> – - v6.3 (Sep. 2011) from WUSTL - - <LI> <B>Coelacanth</b> (<em>Latimeria chalumnae</em>) <b>latCha1</b> – - LatCha1 (Aug. 2011) from the Broad Institute - - <LI> <B>Nile tilapia</b> (<em>Oreochromis niloticus</em>) <b>oreNil2</b> – - OreNil1.1 (Jan. 2011) from the Broad Institute - </UL> - <p> - Our sincere thanks to the many organizations who contributed to the release - of these datasets. We'd also like to acknowledge the Genome Browser - staff who worked on this release: Hiram Clawson, Chin Li, Brian Raney, - Brooke Rhead, Steve Heitner, Pauline Fujita, Luvina Guruvadoo, Greg Roe, and - Donna Karolchik. Please see the Genome Browser - <a href="goldenPath/credits.html">credits page</a> for complete acknowledgment - information and data use restrictions. All datasets may be downloaded from our - <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/">ftp server</a> or - <a href="http://hgdownload.cse.ucsc.edu/downloads.html">downloads</a> page. - </p> - <p> - We regret that we don't have the resources to support the many other - genomics research communities who would like us to visualize their data - in our browser. However, we can provide you with information for setting up - your own browser or track hub to display your data, as well as links to - other visualization resources on the web that are specific to your - genome of interest. Feel free to contact our - <a href="contacts.html">mail list</a> for more information. - </p> - <p> - *Lindblad-Toh K <em>et al</em>. - <a href="http://www.nature.com/nature/journal/v478/n7370/full/nature10530.html" - target="_blank">A high-resolution map of human evolutionary constraint using 29 - mammals</a>. <em>Nature</em>. 2011 Oct 12;478(7370):476-82. - </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>