9531fa7cf8d580673e0f0741c033e83c6a10d519 luvina Tue Mar 5 14:57:02 2013 -0800 added dbSNP 137 mm10 announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 59fb118..4908eb1 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,83 +14,88 @@

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- 11 February 2013 - - Denisova tracks released on hg19 browser + 05 March 2013 + - dbSNP 137 Available for mm10
- In conjunction with the publication of the paper by Meyer et al. - - A High-Coverage Genome Sequence from an Archaic Denisovan Individual - the UCSC Genome Browser is hosting a set of new tracks. Briefly, Meyer et al. - applied a novel single-stranded DNA library preparation method to DNA previously - extracted from 40mg of a phalanx bone excavated from Denisova Cave in the - Altai Mountains in southern Siberia. +

+ We are pleased to announce the release of three tracks derived + from dbSNP build 137, available on the mouse assembly (GRCm38/mm10). + dbSNP build 137 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.

- Two supporting datasets and one analysis dataset are now available in the Genome Browser: + As for dbSNP build 137, there are three tracks in this release. + One is a track containing all mappings of reference SNPs to the + mouse assembly, labeled "All SNPs (137)". The other two tracks + are subsets of this track and show interesting and easily defined + subsets of dbSNP:

    -
  • Modern Human Variants: variant calls made from sequence reads of eleven individuals - mapped to the human genome, used in statistical analyses to put the divergence of the - Denisova genome into perspective with regard to present-day humans. -
  • Denisova Sequence: high-coverage (30X) sequence reads from an archaic Denisovan - individual mapped to the human genome reference assembly. -
  • Modern Human Derived, Denisova Ancestral: mutations in the modern human lineage - that rose to fixation or near fixation since the split from the last common - ancestor with Denisovans, along with predicted functional effects from Ensembl's - Variant Effect Predictor (VEP). +
  • Common SNPs (137): uniquely mapped variants that appear in + at least 1% of the population +
  • Mult. SNPs (137): variants that have been mapped to more + than one genomic location

- We'd like to thank Richard Green and the many authors of the Science paper - for providing the UCSC Genome Browser with these data. - We'd also like to acknowledge the hard work of the UCSC Genome Browser staff - who pulled together the annotations and information for these tracks: - Angie Hinrichs and Pauline Fujita. + By default, only the Common SNPs (137) are visible; other + tracks must be made visible using the track controls. +

+

+ You will find the three SNPs (137) tracks on the Mouse Dec. + 2011 (GRCm38/mm10) browser in the "Variation and Repeats" group. +

+ The tracks were produced at UCSC by Angie Hinrichs and Luvina Guruvadoo.

+ +

+ 11 February 2013 - + Denisova tracks released on hg19 browser + In conjunction with the publication of the paper by Meyer et al. + + A High-Coverage Genome Sequence from an Archaic Denisovan Individual + the UCSC Genome Browser is hosting a set of new tracks. + Read more. +

+

25 January 2013 - Southern White Rhinoceros Genome Browser Release: We are pleased to announce the release of a Genome Browser for the May 2012 assembly of the Southern White Rhinoceros, Ceratotherium simum simum (Broad Institute version cerSimSim1.0, UCSC version cerSim1). Read more.

22 January 2013 - New Baboon (papAnu2) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the March 2012 assembly of the Olive Baboon, Papio anubis (Baylor Panu_2.0, UCSC version papAnu2). Read more.

-

- 15 January 2013 - - New Lamprey (petMar2) Assembly Now Available in the Genome Browser: - We are pleased to announce the release of a Genome Browser for the September 2010 - assembly of the Lamprey, Petromyzon marinus (WUGSC 7.0, UCSC version - petMar2). - Read more. -

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