The UCSC Genome Browser database: update 2010

Abstract

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.

Figure 1.

Main Genome Browser display page on the hg18 human assembly, showing the Wiki track, OMIM Genes, UCSC Genes and the 44-species Conservation track, with all six conservation score tracks visible. The highlighted region shows drag-and-zoom in action. When the mouse button is released, the browser will redraw at the new coordinates listed in the position/search box.

Figure 2.

Details page of SNP rs4987121 from the SNPs (130) track, showing the new ‘predicted function relative to selected gene tracks’ feature using UCSC Genes, RefSeq Genes and Ensembl Genes. The window on the right is the Chimera 3D protein structure viewer, opened by clicking on the ‘Chimera’ link in the first window. The selected SNP is highlighted in red, while other non-synonymous SNPs are highlighted in gold.