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Oxford University Press, Nucleic Acids Research, D1(44), p. D717-D725, 2015

DOI: 10.1093/nar/gkv1275

Oxford University Press, Nucleic Acids Research, D1(43), p. D670-D681, 2014

DOI: 10.1093/nar/gku1177

Oxford University Press, Nucleic Acids Research, D1(42), p. D764-D770, 2013

DOI: 10.1093/nar/gkt1168

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The UCSC genome browser database: 2008 update

Journal article published in 2007 by D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs ORCID, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 provide an integrated environment for visualizing, comparing, analysing 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 ∼90 organisms. 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.