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. 2006 Jan 1;34(Database issue):D590-8.
doi: 10.1093/nar/gkj144.

The UCSC Genome Browser Database: update 2006

A S Hinrichs  1 , D Karolchik, R Baertsch, G P Barber, G Bejerano, H Clawson, M Diekhans, T S Furey, R A Harte, F Hsu, J Hillman-Jackson, R M Kuhn, J S Pedersen, A Pohl, B J Raney, K R Rosenbloom, A Siepel, K E Smith, C W Sugnet, A Sultan-Qurraie, D J Thomas, H Trumbower, R J Weber, M Weirauch, A S Zweig, D Haussler, W J Kent
Affiliations

The UCSC Genome Browser Database: update 2006

A S Hinrichs et al. Nucleic Acids Res. .

Abstract

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

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Figures

Figure 1
Figure 1
Genome Browser zoomed in to base-level view, showing Base Position, Restriction Enzymes, sno/miRNA, Conservation and SNP tracks at chr19:58, 982, 732-58, 982, 815 in the May 2004 assembly of the human genome. At this location is microRNA hsa-mir-371, portions of which are found to be highly conserved in other mammals by phastCons (8). In the Conservation track, gaps in the human sequence with respect to other species in the alignment are indicated by small orange vertical bars between bases in the other species, with gap lengths indicated by orange numbers in the ‘Gaps’ row.
Figure 2
Figure 2
Genome Browser, zoomed out to view all of human chromosome 21 in the May 2004 assembly. A title line and assembly/position line have been added using the Base Position track's new label options. Large gaps show the location of unsequenced heterochromatin. Most tracks are in ‘dense’ display mode, so that all items are condensed into a single row. The Known Genes track is in ‘squish’ mode so that individual features are drawn at half-height; this gives an idea of gene density when viewing large regions. The cross-species Net tracks are in ‘full’ mode so that the hierarchy of alignments to each other species is clear. Human chromosome 21 contains two ENCODE regions (shown in ‘pack’ mode), in which dozens of additional tracks are available. This image is not a screen snapshot but rather a PostScript image generated by the Genome Browser.
See this image and copyright information in PMC

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References

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