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The UCSC Genome Browser database: 2015 update.

  • Author(s): Rosenbloom, Kate R
  • Armstrong, Joel
  • Barber, Galt P
  • Casper, Jonathan
  • Clawson, Hiram
  • Diekhans, Mark
  • Dreszer, Timothy R
  • Fujita, Pauline A
  • Guruvadoo, Luvina
  • Haeussler, Maximilian
  • Harte, Rachel A
  • Heitner, Steve
  • Hickey, Glenn
  • Hinrichs, Angie S
  • Hubley, Robert
  • Karolchik, Donna
  • Learned, Katrina
  • Lee, Brian T
  • Li, Chin H
  • Miga, Karen H
  • Nguyen, Ngan
  • Paten, Benedict
  • Raney, Brian J
  • Smit, Arian FA
  • Speir, Matthew L
  • Zweig, Ann S
  • Haussler, David
  • Kuhn, Robert M
  • Kent, W James
  • et al.
Abstract

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

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