The UCSC Genome Browser database: 2015 update

The UCSC Genome Browser database: 2015 update

2015, Vol. 43, Database issue | Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Donna Karolchik, 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 and provide comprehensive resources for genome assemblies and annotations. Key highlights of the past year include the release of a new human genome reference assembly (GRCh38, UCSC hg38) after a 4-year gap, a significant comparative genomics annotation, and a novel distribution mechanism (GBiB: Genome Browser in a Box). New species browsers were created for the Chinese hamster, elephant shark, and minke whale, and DNA sequences were mined from the web. The browser display was enhanced with stacked color graphs and region highlighting. The user community increasingly adopts UCSC's track hub and assembly hub representations for sharing large-scale genomic data sets and sequencing projects, tripling the number of public data hubs. The article also details the process of creating a new genome browser, including downloading sequences, verifying consistency, creating chromosome sequences, analyzing repetitive elements, and aligning to other species. Future plans include expanding the hg.38 human genome browser, incorporating gene expression and regulatory data, and developing a graphical network browser.The UCSC Genome Browser database, launched in 2001, continues to grow and provide comprehensive resources for genome assemblies and annotations. Key highlights of the past year include the release of a new human genome reference assembly (GRCh38, UCSC hg38) after a 4-year gap, a significant comparative genomics annotation, and a novel distribution mechanism (GBiB: Genome Browser in a Box). New species browsers were created for the Chinese hamster, elephant shark, and minke whale, and DNA sequences were mined from the web. The browser display was enhanced with stacked color graphs and region highlighting. The user community increasingly adopts UCSC's track hub and assembly hub representations for sharing large-scale genomic data sets and sequencing projects, tripling the number of public data hubs. The article also details the process of creating a new genome browser, including downloading sequences, verifying consistency, creating chromosome sequences, analyzing repetitive elements, and aligning to other species. Future plans include expanding the hg.38 human genome browser, incorporating gene expression and regulatory data, and developing a graphical network browser.
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