title: The UCSC Genome Browser database: 2014 update.
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.
authors.affiliation: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.
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authors.lastname: Dreszer
authors.forename: Pauline A
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authors.lastname: Guruvadoo
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authors.lastname: Haeussler
authors.forename: Rachel A
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authors.lastname: Heitner
authors.forename: Angie S
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authors.forename: Katrina
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authors.lastname: Learned
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authors.forename: Brian J
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authors.lastname: Rosenbloom
authors.forename: Cricket A
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authors.lastname: Sloan
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Speir
authors.forename: Ann S
authors.initials: AS
authors.lastname: Zweig
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authors.lastname: Haussler
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mesh_terms: D000483:Alleles; D000818:Animals; D030541:Databases, Genetic; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D012984:Software