f877f97befd2b2b0ffbcc69ae83fa77689e3fb9f mspeir Wed Sep 4 10:10:59 2013 -0700 Adding announcement about oviAri3 release, refs #9409 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index f45fa18..356148c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,159 +1,85 @@
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- 22 August 2013 - - Three New Human Variation Tracks Released -

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- We are pleased to announce the release of three tracks that describe - human genetic variation. They are based on the - Leiden Open - Variation Database (LOVD), the - Human Gene - Mutation Database Public (HGMD), and amino acid mutations in the - UniProt database. The - majority of the data were collected from publications by curators in the three - databases. -

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- The three databases have varying license restrictions. UniProt provides complete - information about the mutation amino acid change, the disease and a link to the - publications that mention it. LOVD provides the mutation and a link to a website - with disease and publication details. HGMD provides some coordinates and a link to - its own website which requires registration. -

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- These tracks are intended for use primarily by physicians and other professionals - concerned with genetic disorders, by genetics researchers, and by advanced students - in science and medicine. While the Genome Browser database is open to the public, users - seeking information about a personal medical or genetic condition are urged to consult - with a qualified physician for diagnosis and for answers to personal questions. -

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- We'd like to thank all three databases for their help in putting the data together. The - tracks were produced at UCSC by Maximilian Haeussler and Steve Heitner. -

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- 22 July 2013 - - Variant Annotation Integrator -

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- In order to assist researchers in annotating and prioritizing thousands - of variant calls from sequencing projects, we have developed the Variant - Annotation Integrator (VAI). Given a set of variants uploaded as a - custom track (in either pgSnp - or VCF format), the VAI will - return the predicted functional effect (e.g., synonymous, missense, - frameshift, intronic) for each variant. The VAI can optionally add - several other types of relevant information, including: the - dbSNP - identifier if the variant is found in dbSNP, protein damage scores for - missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP), - and conservation scores computed from multi-species alignments. The VAI - also offers filters to help narrow down results to the most interesting - variants. -

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- Future releases of the VAI will include more input/upload options, - output formats, and annotation options, and a way to add information - from any track in the Genome Browser, including custom tracks. -

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- There are two ways to navigate to the VAI: (1) From the "Tools" - menu, follow the "Variant Annotation Integrator" link. (2) - After uploading a custom track, hit the "go to variant annotation - integrator" button. The user's guide is at the bottom of the page, - under "Using the Variant Annotation Integrator." -

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- Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and - Jonathan Casper for their input and work on this feature. + 05 September 2013 - + New Sheep (oviAri3) Assembly Now Available in the Genome Browser +

+ We are pleased to announce the release of a Genome Browser for the August 2012 + assembly of sheep, Ovis aries (ISGC Oar_v3.1, UCSC version + oviAri3). The whole genome shotgun assembly was provided by the + International Sheep Genomics Consortium. + There are 5,698 scaffolds with a total size of 2,619,054,388 bases. +

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+ 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. + The sheep (oviAri3) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + Credits page for a detailed + list of the organizations and individuals who contributed to this release.

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- 2 July 2013 - - Assembly Data Hubs: Assembly Data Hubs extend the - functionality of Track Data Hubs to assemblies that are not hosted - natively on the Browser. - Read more. -

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- 2 July 2013 - - New Gene Alleles feature on the details pages of UCSC genes: - For each protein-coding gene in the UCSC Genes track, variant data from - the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000 - Genomes Project have been distilled into "gene haplotype - alleles." - Read more. -

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