33a7f9d512c35cea0076b5b9e1cbd605e00143d2 kuhn Wed Feb 29 10:58:10 2012 -0800 added snp135 annoucement and archived one other diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 37f6afd..6cb1f2e 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,116 +1,159 @@
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+ 10 February 2012 + - dbSNP 135 Available for hg19 +

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. +

+

+ 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: +

+ +
    +
  • Common SNPs (135): uniquely mapped variants that appear in + at least 1% of the population +
  • Flagged SNPs (135): uniquely mapped variants, excluding + Common SNPs, that have been flagged by dbSNP as "clinically + associated" +
  • Mult. SNPs (135): variants that have been mapped to more + than one genomic location +
+ +

By default, only the Common SNPs (135) are visible; other + tracks must be made visible using the track controls. +

+ +

You will find the four SNPs (135) tracks on the Human Feb. + 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group. +

+ +

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. +

+ + 2 February 2012 - New UCSC Genes Track Released for GRCh37/hg19

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:

  • 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.

Additionally, several improvements where made to the UCSC Genes build pipeline:

  • 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.

More details about the new UCSC Genes track can be found on the - UCSC Genes track description page. + 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.

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