The UCSC Genome Browser database: 2015 update

The UCSC Genome Browser database: 2015 update

2015 | Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadvo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Katrina Learned, Brian T. Lee, Chin H. Li, Karen H. Miga, Ngan Nguyen, Benedict Paten, Brian J. Raney, Arian F. A. Smit, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn and W. James Kent
The UCSC Genome Browser database, launched in 2001, continues to grow as a comprehensive resource for genome assemblies and annotations. In 2015, the database was updated with new features, including a browser for the first new human genome reference assembly in four years (GRCh38, UCSC hg38), a major comparative genomics annotation for 100 species, and a new distribution mechanism called GBiB (Genome Browser in a Box). New browsers were created for species such as the Chinese hamster, elephant shark, and minke whale. The database now includes 160 genome assemblies from 91 species, with extensive annotations from RefSeq, GENCODE, Ensembl, and other sources. The UCSC bioinformatics group provides a range of tools, including BLAT and liftOver/chain/net for genome coordinate conversion. The database also hosts data from the Neanderthal and Denisova genome projects and all ENCODE data from the first 11 years of the project. The UCSC Genome Browser offers a flexible, high-performance web interface for visualizing genomic annotations, with features such as stacked color graphs, region highlighting, and customizable track configurations. New data includes updated human and mouse gene sets, new regulatory annotations, and expanded gene expression data. The database also includes new genome browsers for several species, including the rat, Ebola virus, and three newly sequenced animals. The database now supports public track and assembly hubs, allowing users to share and access genomic data. The UCSC Genome Browser also provides tools for data mining, including the Table Browser and Variant Annotation Integrator (VAI). The database includes a wide range of genomic data, including gene models, epigenetic annotations, and comparative genomics data. The database is continuously updated with new annotations and data, and users can access it through the UCSC Genome Browser website. The database is also available as a downloadable package (GBiB) for academic and non-profit use. The UCSC Genome Browser is a valuable resource for researchers and students in the fields of genomics, genetics, and biomedical research.The UCSC Genome Browser database, launched in 2001, continues to grow as a comprehensive resource for genome assemblies and annotations. In 2015, the database was updated with new features, including a browser for the first new human genome reference assembly in four years (GRCh38, UCSC hg38), a major comparative genomics annotation for 100 species, and a new distribution mechanism called GBiB (Genome Browser in a Box). New browsers were created for species such as the Chinese hamster, elephant shark, and minke whale. The database now includes 160 genome assemblies from 91 species, with extensive annotations from RefSeq, GENCODE, Ensembl, and other sources. The UCSC bioinformatics group provides a range of tools, including BLAT and liftOver/chain/net for genome coordinate conversion. The database also hosts data from the Neanderthal and Denisova genome projects and all ENCODE data from the first 11 years of the project. The UCSC Genome Browser offers a flexible, high-performance web interface for visualizing genomic annotations, with features such as stacked color graphs, region highlighting, and customizable track configurations. New data includes updated human and mouse gene sets, new regulatory annotations, and expanded gene expression data. The database also includes new genome browsers for several species, including the rat, Ebola virus, and three newly sequenced animals. The database now supports public track and assembly hubs, allowing users to share and access genomic data. The UCSC Genome Browser also provides tools for data mining, including the Table Browser and Variant Annotation Integrator (VAI). The database includes a wide range of genomic data, including gene models, epigenetic annotations, and comparative genomics data. The database is continuously updated with new annotations and data, and users can access it through the UCSC Genome Browser website. The database is also available as a downloadable package (GBiB) for academic and non-profit use. The UCSC Genome Browser is a valuable resource for researchers and students in the fields of genomics, genetics, and biomedical research.
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[slides and audio] The UCSC Genome Browser database%3A 2015 update