The UCSC Genome Browser database: 2015 update

Abstract

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

Figure 1.

Genome Browser screenshot of the transcription start site of the ZFX gene illustrating the new stacked color graph display. The enrichment of histone marks H3K4me1, H3K4me3 and H3K27ac is shown in three browser tracks, where contribution to the sum of the signal by each of the six different cell types is indicated by color. Note that the K3K4me1 signal is low in all cell types across the promoter and at the beginning of the transcript, but high on either side of the promoter. The other two marks show the opposite tendency, being highest at the promoter and declining with distance from the promoter. In general the signals are strongest in the turquoise cell line (HUVEC).

Figure 2.

Genome Browser image of interspersed repeat (IR) annotation on a short region of the human assembly hg38 using the new visualization track. This region contains several layers of nested IRs, created when transposable elements insert into and break up older IR sequences. The solid lines join aligned fragments of an IR and can often reveal interesting features of a locus such as target site duplications. The dashed lines represent the unaligned portions of the transposable element sequence and allow one to visually decipher the relative consensus position of the fragments. When it is not practical to draw the unaligned sequence to scale, the length is displayed between two hash marks. Each annotation box encodes the class of the repeat using the colored edge, the divergence of the repeat with the grayscale interior fill color (lighter levels of gray indicate higher divergence) and the orientation of the repeat using arrowheads.