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To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. + 22 July 2013 + - Variant Annotation Integrator + ++ 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. + ++ 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. + ++ 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." + ++ Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and + Jonathan Casper for their input and work on this feature. + + +2 July 2013 - Assembly Data Hubs We are pleased to announce a new feature in the UCSC Genome Browser: Assembly Data Hubs. Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. Assembly Data Hubs were developed to address the increasing need for researchers to annotate sequence for which UCSC does not provide an annotation database. They allow researchers to include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are @@ -47,127 +85,76 @@ To read more about using Assembly Data Hubs, or about creating your own, please see these guides: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html http://genomewiki.ucsc.edu/index.php/Assembly_Hubs Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature. + + +- 2 July 2013 - - New Gene Alleles feature on the details pages of UCSC genes - -- We are excited to announce the release the 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." Each haplotype allele is a - distinct set of variants found on at least one of the 1000 Genomes - subject chromosomes. For each haplotype, we display its frequency in - the 1000 Genomes populations and indicate the frequency with which it - occurs homozygously in each population. Unexpected frequencies of - occurrence may thus be used to identify alleles that merit further - study. Predicted protein sequence for common haplotypes can also be - displayed, allowing differences among alleles to be used to identify - differences at the amino acid level. - -- To see the Gene Alleles feature, go to the details page for any - protein-coding gene in the UCSC Genes track and click the "Gene - Alleles" link in the top right cell of the "Page Index" matrix. This - will take you to the "Common Gene Haplotype Alleles" section. For - more information on this feature please see this help doc: - -- - http://genome.ucsc.edu/goldenPath/help/haplotypes.html - + +- We're happy to announce the release of an updated UCSC Genes - track for the GRCh37/hg19 human Genome Browser. - The new release has 82,960 total transcripts, compared with - 80,922 in the previous version. The total number of canonical - genes has increased from 31,227 to 31,848. Comparing the new - gene set with the previous version: -
- More details about the new UCSC Genes track can be found on - the UCSC Genes track description page. - -- Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo - for their work on this track! + 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. - - - + 28 June 2013 + - 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. + Read more. + 27 June 2013 - New Official European Mirror Released: Announcing an official mirror for European users, with automatic redirection. Read more. 26 June 2013 - Suggestion Box Released: Due to popular demand, we have created a suggestion box for track, assembly, tool, and other feature requests. Read more. - - - |