08719591eedceaa39a0067492592428af89f1f91 donnak Thu Feb 2 19:59:37 2012 -0800 Added announcement for new hg19 UCSC Genes track. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8fd76e4..37f6afd 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,64 +14,96 @@ </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 --> -<!-- Wallaby Assembly release --> - <FONT FACE="courier" SIZE="3"><B>23 January 2012 - Wallaby Browser Available</B></FONT> + <FONT FACE="courier" SIZE="3"><B>2 February 2012 - New UCSC + Genes Track Released for GRCh37/hg19</B></FONT> <P> - We have released a Genome Browser for the September 2009 - genome assembly of the Tammar Wallaby, <em>Macropus - eugenii</em> (TWGS version Meug_1.1, UCSC version macEug2). This assembly, - which has been sequenced to 2X coverage, was produced by - the Tammar Wallaby Genome Sequencing Consortium, a collaboration - between the Baylor College of Medicine - <a href="http://www.hgsc.bcm.tmc.edu/project-species-m-Wallaby.hgsc" - target="_blank"> Human Genome Sequencing Center</a> and the - <a href="http://www.agrf.org.au/default.aspx" - target="_blank">Australian Genome Research Facility</a>. - + We're happy to announce the release of an updated UCSC Genes + track for the GRCh37/hg19 human Genome Browser. This release + includes more noncoding transcripts based on data from + <A HREF="http://rfam.sanger.ac.uk/" TARGET=_blank>Rfam</A> + and from the + <A HREF="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=tRNAs">tRNA Genes track</A> + contributed by the <A HREF="http://lowelab.ucsc.edu/" + TARGET=_blank>Todd Lowe lab</A> at UCSC. + <P> + The new release has 80,922 total transcripts, compared with + 77,614 in the previous version. The total number of + canonical genes has increased from 27,297 to 31,227. + Comparing the new gene set with the previous version: + <UL> + <LI>24,804 transcripts did not change between versions. + <LI>483 transcripts were not carried forward to the new + version. + <LI>46,367 transcripts are "compatible" with those in the + previous set, meaning that the two transcripts show + consistent splicing. In most cases, the old and new + transcripts differ in the lengths of their UTRs. + <LI>5,960 transcripts overlap with those in the previous + set but do not show consistent splicing, i.e., they contain + overlapping introns with differing splice sites. + </UL> <P> - Bulk downloads of the sequence and annotation data are - available via the Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/">FTP server</A> - or the - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#wallaby">Downloads</A> - page. These data have - <A HREF="goldenPath/credits.html#wallaby_use">specific - conditions for use</A>. + Additionally, several improvements where made to the UCSC + Genes build pipeline: + <UL> + <LI>We developed new genomic alignment protocols for + aligning short sequences, facilitating the expansion of the + noncoding RNA content. + <LI> + We changed the way that gene symbols are assigned to + transcripts so that names from curated sources are favored + over names coming directly from GenBank mRNA records. This + change resolved several confusing naming issues reported to + us by users. + <LI>We tracked down and corrected a bug in the pipeline that + was causing a number of poor quality protein mappings to + displace high quality protein mappings. + <LI>We have started producing two new tables, + knownGeneTxMrna and knownGeneTxPep, that contain sequence + derived from the genome rather than from the mRNA used for + the transcript. + </UL> <P> - We'd like to thank the Tammar Wallaby Genome Sequencing Consortium for - providing this assembly. The wallaby Genome Browser and annotation - tracks were produced by Chin Li and Luvina Guruvadoo. See the - <A HREF="goldenPath/credits.html#wallaby_credits">Credits</A> - page for a detailed list of the organizations and - individuals who contributed to this release. + More details about the new UCSC Genes track can be found on the + <A HREF="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes track description page</A>. + <P> + Many thanks to Melissa Cline, Jim Kent, Brian Raney, Mark + Diekhans, and Brooke Rhead for their work on this track! <P> <HR> <!-- start archives --> + <FONT FACE="courier" SIZE="3"><B>23 January 2012 - Wallaby + Browser Available: </B></FONT> + We have released a Genome Browser for the September 2009 + genome assembly of the Tammar Wallaby, <em>Macropus + eugenii</em> (TWGS version Meug_1.1, UCSC version macEug2). + <A HREF="goldenPath/newsarch.html#230112">Read more</A>. + <P> <FONT FACE="courier" SIZE="3"><B>3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington University: </B></FONT> We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our Data Hub function. <A HREF="goldenPath/newsarch.html#030112">Read more</A>. <P> <FONT FACE="courier" SIZE="3"><B>19 December 2011 - Variant Call Format (VCF) Now Supported in Genome Browser: </B></FONT> We are pleased to announce that the UCSC Genome Browser now supports Variant Call Format (VCF). <A HREF="goldenPath/newsarch.html#191211">Read more</A>. </P> <P>