The UCSC Genome Browser Database: update 2009

Abstract

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

Figure 1.

SNP 129 track details page showing partial information about SNP rs1128456 on chromosome 1.

Figure 2.

Screen image of Genome Browser for hg18 human assembly, chromosome 1, showing several new features. From top to bottom: Scale bar; UCSC Genes track; Non-human RefSeq Genes; TransMap RefSeq Genes, showing improved mapping of bases at 3′-end of a mouse RefSeq (red) that did not map in Non-Human RefSeq track; Conservation track; SNP 129 track. Entire image has been reversed from default configuration using Reverse button (cursor arrow at bottom) to show Transmap annotations in 5′-to-3′ direction.

Figure 3.

Gene Sorter output showing new columns for the TP53 gene (top row) and all genes meeting the criterion, Protein Homology–BLASTP. Columns shown, left to right: BLASTP E-value, Genome Position, Exon Count, Intron Size (set to maximum size) and Coding SNPs (truncated).