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UCSC Genome Browser


NAR Molecular Biology Database Collection entry number 316
Tyner, Cath1, Barber, Galt P.1, Casper, Jonathan1, Clawson, Hiram1, Diekhans, Mark1, Eisenhart, Christopher 1, Fischer, Clayton M.1, Gibson, David1, Navarro Gonzalez, Jairo1, Guruvadoo, Luvina1, Haeussler, Maximilian1, Heitner, Steve 2, Hinrichs, Angie S.1, Karolchik, Donna1, Lee, Brian T.1, Lee, Christopher M.1, Nejad, Parisa1, Raney, Brian J.1, Rosenbloom, Kate R.1, Speir, Matthew L.1, Villarreal, Chris1, Vivian, John1, Zweig, Ann S.1, Haussler, David1,3, Kuhn, Robert M.1, and Kent, W. James1
1Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA 2 Emory University School of Medicine, Atlanta, Georgia 30322, USA 3 Howard Hughes Medical Institute, University of California 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 2016, the database contained genomic sequence and a basic set of annotation ‘tracks’ for 96 unique species, 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 2015-16 timeframe, three new species assemblies were added (brown kiwi, aptMan1; crab-eating macaque, macFas5; Malayan flying lemur, galVar1) and new assembly versions were added for the following eight species: C. elegans (ce11), cat (felCat8), chicken (galGal5), gray mouse lemur (micMur2), platypus (ornAna2), rhesus macaque monkey (rheMac8), western clawed frog (xenTro7), and western gorilla (gorGor4). Support for new data types include CRAM, RNA-Seq expression data, and long-range chromatin interaction pairs. The GENCODE Genes set is now the default gene set for the latest GRCh38/hg38 human assembly, replacing the previous default set, UCSC Genes. Updated UCSC Genes tracks are available for human and mouse. A new 100-vertebrate conservation track was released on the hg38 human assembly that compares pairwise alignments for 100 species from a variety of clades. The C. elegans (ce11) 26-species conservation track was added, which shows the multiple alignments and measurements of evolutionary conservation for 26 nematode species. New user-interface changes include newly designed home and gateway pages as well as a new “multi-region” track display configuration for exon-only, gene-only, and custom regions visualization. The ability to make sessions public or add sessions to a new "public sessions gallery" was added. To assist users who are geographically closer to Asia, this year's changes include the unveiling of a new supported mirror site in Japan. Thirteen public hubs were also added.

Acknowledgements

Sincere gratitude is extended to the worldwide users of the UCSC Genome Browser, from college students who are just beginning their journey to experienced researchers. Special appreciation is extended to funders, collaborators, and contributors who give value beyond measure to the research possibilities within the browser. Much thanks is given to the exceptional group of system administrators, the management team, and all staff who support the UCSC Genome Browser.

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