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The UCSC Genome Browser database


NAR Molecular Biology Database Collection entry number 316
Karolchik, D.1, Barber, G.P.1, Casper, J.1, Clawson, H.1, Cline, M.S.1, Diekhans, M.1, Dreszer, T.R.1, Fujita, P.A.1, Guruvadoo, L.1, Haeussler, M.1, Harte, R.A.1, Heitner, S.1, Hinrichs, A.S.1, Learned, K.1, Lee, B.T.1, Li, C.H.1, Raney, B.J.1, Rhead, B.2, Rosenbloom, K.R.1, Sloan, C.A.3, Speir, M.L.1, Zweig, A.S.1, Haussler, D.1, 4, Kuhn, R.M.1, and Kent, W.J.1
1 Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA 2 Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA 3 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA 4 Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA

Database Description

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s Web-based tools – including Blat, the Table Browser, VisiGene, the Gene Sorter, Genome Graphs, and the Variant Annotation Integrator -- provide an integrated environment for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation ‘tracks’ for nearly 90 organisms, many with multiple assembly versions. Most genome assemblies offer mapping and sequence annotation tracks describing assembly, gap, and GC content, and alignments of mRNA, EST, and RefSeq data from GenBank. Some assemblies provide additional gene annotations and sequence alignments of selected species to facilitate comparative and evolutionary investigations. The heavily annotated human genome offers extensive conservation and evolutionary comparisons, a large collection of gene models, regulation, expression, epigenetics and tissue differentiation, variation, phenotype and disease association data, and text-mined data from publications. In addition to the native data sets local to the UCSC servers, the Genome Browser offers several options to users for viewing their own sequence and annotations: track and assembly data hubs, custom tracks, and sessions. The Genome Browser database and tools may also be installed on a local server for customized use. The full set of data, software tools, downloads, and documentation can be found on the Genome Browser website.

Recent Developments

During the 2012-13 timeframe, 35 vertebrate assemblies were added to the Genome Browser, including the premier releases of 19 species: 4 primates (baboon, mouse lemur, squirrel monkey, and tarsier), 11 additional mammals (alpaca, dolphin, ferret, hedgehog, kangaroo rat, manatee, megabat, rock hyrax, shrew, sloth, southern white rhinoceros, and tree shrew), and 4 additional vertebrates (American alligator, Atlantic cod, budgerigar, and coelacanth). Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes, and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Acknowledgements

The authors would like to thank the many data contributors and collaborators whose work makes the Genome Browser possible, our Scientific Advisory Board for guiding our efforts, our users for their consistent support and valuable feedback, and our outstanding team of system administrators: Jorge Garcia, Erich Weiler, and Gary Moro.

References

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