The UCSC Genome Browser database: extensions and updates 2013

Abstract

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

Figure 1.

Genome Browser image of the promoter region of DARC on human assembly hg19 including UCSC Genes, dbSNP 135 and the Publications track showing sequences and SNPs text-mined from PubMed Central and Elsevier. The region shown includes a SNP responsible for the Duffy blood group (rs2814778). The publication track contains sequences in this region from several articles relevant to this SNP. Note that hovering the mouse over a sequence shows the title of the corresponding article. Clicking on a sequence in the publications track takes the user to a page with details about the relevant article.

Figure 2.

Genome Browser image of the promoter region and transcription start of IRF1 on human assembly hg19 showing UCSC Genes, 1000 Genomes Phase 1 Integrated Variant Calls in the haplotype sorting VCF display mode, histone mark H3K27Ac binding in overlays of 7 ENCODE cell lines and PhyloP conservation scores from alignments of placental mammals. Mouse-over text gives the dbSNP identifier and genotype counts for one of the 1000 Genomes variants. The variant outlined in purple is used as the center variant for clustering haplotypes by similarity, and is clearly in linkage with nearby variants. Wider purple triangular leaves of the clustering tree indicate more common local haplotypes. Note that the reference genome haplotype (horizontal run of invisible reference alleles) is often not the major haplotype among the 1000 Genomes Phase 1 samples.