The UCSC Genome Browser database: update 2011

Abstract

The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

Figure 1.

Genome Browser display on the hg19 human assembly showing the gene search box in use. After two or more characters are typed, the software suggests possible matching gene names. Tracks shown in this image, from top to bottom: base position, GNF Atlas 2 (with the red/blue on yellow background microarray color option enabled), SNPs (131) and Genome Variants (which includes five new datasets).

Figure 2.

Genome Browser image on the hg18 human assembly showing the UCSC Genes, Conservation and Neandertal tracks (Human-Chimp coding differences, regions with the 5% lowest S, SNPs used to calculate S and alignments of Neandertal sequence reads). The Vi33.6 sequence read subtrack highlighted in green is being vertically dragged to a new position. Note that hovering the mouse over any component subtrack causes the vertical bars to the left of all related subtracks to turn blue.