The UCSC Genome Browser database: 2014 update

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 large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Figure 1.

The haplotype alleles display for the ABO gene, which encodes proteins related to the ABO blood group system. A large portion of the ‘Predicted full sequence’ section is truncated in the upper image for display purposes, and is shown in greater detail in the lower image. The leftmost columns of the top image indicate the frequency of each allele haplotype within the 1000 Genomes sample and the occurrence of homozygosity for each allele. In this instance the haplotype alleles display has been expanded to show the distribution of the haplotypes across the major 1000 Genomes population groups. The ‘Variant Sites’ columns summarize the non-synonymous variant sites that occur in at least 1% of the subject chromosomes, with the value from the reference genome (in this case GRCh37/hg19) indicated at the top of each variant column. In all but one case, the ‘O’ phenotype results from a common insertion (indicated by ‘-’ in the reference) causing a frameshift (indicated by ‘[≫]’) that results in a downstream premature stop codon, thus truncating the protein. Note that although certain haplotyes are more frequently found within one population, the insertion that gives rise to the majority of ‘O’ phenotypes is found across all populations, which may indicate that the insertion predates the most recent migration out of Africa. On the other hand, the haplotype in which the SNP variant introduces a stop codon at the variant site may have arisen in the Americas. The zoomed-in view of the ‘Predicted full sequence’ section in the bottom image shows the reference sequence (top row) and sequences incorporating the common non-synonymous variants. The residues corresponding to the variant sites are highlighted by green vertical bars, the site corresponding to the frameshift-causing insertion is highlighted by a blue bar and changes to the reference amino acid sequence are shown in red.