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 @@

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- - 23 January 2012 - Wallaby Browser Available + 2 February 2012 - New UCSC + Genes Track Released for GRCh37/hg19

- We have released a Genome Browser for the September 2009 - genome assembly of the Tammar Wallaby, Macropus - eugenii (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 - Human Genome Sequencing Center and the - Australian Genome Research Facility. - + 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 + Rfam + and from the + tRNA Genes track + contributed by the Todd Lowe lab at UCSC. +

+ 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: +

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  • 24,804 transcripts did not change between versions. +
  • 483 transcripts were not carried forward to the new + version. +
  • 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. +
  • 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. +

- Bulk downloads of the sequence and annotation data are - available via the Genome Browser - FTP server - or the - Downloads - page. These data have - specific - conditions for use. + Additionally, several improvements where made to the UCSC + Genes build pipeline: +

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  • We developed new genomic alignment protocols for + aligning short sequences, facilitating the expansion of the + noncoding RNA content. +
  • + 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. +
  • 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. +
  • 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. +

- 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 - Credits - 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 + UCSC Genes track description page. +

+ Many thanks to Melissa Cline, Jim Kent, Brian Raney, Mark + Diekhans, and Brooke Rhead for their work on this track!

+ 23 January 2012 - Wallaby + Browser Available: + We have released a Genome Browser for the September 2009 + genome assembly of the Tammar Wallaby, Macropus + eugenii (TWGS version Meug_1.1, UCSC version macEug2). + Read more. +

3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington University: We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our Data Hub function. Read more.

19 December 2011 - Variant Call Format (VCF) Now Supported in Genome Browser: We are pleased to announce that the UCSC Genome Browser now supports Variant Call Format (VCF). Read more.