68535aa15e737dd023819e2d80977238d02350f6 luvina Wed Feb 29 12:35:42 2012 -0800 Added new mm10 announcement, collapsed old announcement, removed archived annoucement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 6cb1f2e..d4605fa 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,159 +1,125 @@ <!--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><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></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 --> + <FONT FACE="courier" SIZE="3"><B>05 March 2012 - New Mouse + Browser Available</B></FONT> + <P> + We have released the latest Genome Browser for the December 2011 + Mouse genome assembly produced by the + <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/" TARGET=_blank> + Mouse Genome Reference Consortium</a> (NCBI Build 38, UCSC version mm10). + This version, which includes approximately 2.6 Gb of sequence, + is considered to be "essentially complete". The assembly includes + chromosomes 1-19, X, Y, M (mitochondrial DNA) and chr*_random + (unlocalized) and chrUn_* (unplaced clone contigs). + Note that the UCSC mm10 database contains only the + reference strain C57BL/6J. + <P> + Bulk downloads of the sequence and annotation data are available + via the Genome Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/" + TARGET=_blank>FTP server</a> or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#mouse" TARGET=_blank>Downloads</a> + page. The Mouse browser annotation tracks were generated by UCSC + and collaborators worldwide. See the + <a href="http://hgwdev.cse.ucsc.edu/goldenPath/credits.html#mouse_credits" + TARGET=_blank>Credits</a> page for a detailed list of the + organizations and individuals who contributed to the success of this release. <P> + <HR> + + <!-- more news --> <FONT FACE="courier" SIZE="3"><B>10 February 2012 - dbSNP 135 Available for hg19</B></FONT> <P>We are pleased to announce the release of four tracks derived from dbSNP build 135, available on the human assembly (GRCh37/hg19). dbSNP build 135 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 dbSNP build 132, there are four tracks in this release. One is a track containing all mappings of reference SNPs to the human assembly, labeled "All SNPs (135)". The other three tracks are subsets of this track and show interesting and easily defined subsets of dbSNP: </P> <UL> <LI>Common SNPs (135): uniquely mapped variants that appear in at least 1% of the population <LI>Flagged SNPs (135): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated" <LI>Mult. SNPs (135): variants that have been mapped to more than one genomic location </UL> <P>By default, only the Common SNPs (135) are visible; other tracks must be made visible using the track controls. </P> <P>You will find the four SNPs (135) 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 Mary-Claire King 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 and Brooke Rhead. </P> + <HR> - <!-- more news --> + <!-- start archives --> <FONT FACE="courier" SIZE="3"><B>2 February 2012 - New UCSC - Genes Track Released for GRCh37/hg19</B></FONT> - <P> + Genes Track Released for GRCh37/hg19: </B></FONT> 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> - 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> - 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! + track for the GRCh37/hg19 human Genome Browser. + <A HREF="goldenPath/newsarch.html#020212">Read more</A>. <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> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>