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The UCSC Genome Browser database: 2016 update

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent
doi: https://doi.org/10.1101/027037
Matthew L. Speir
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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  • For correspondence: mspeir@soe.ucsc.edu
Ann S. Zweig
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Kate R. Rosenbloom
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Brian J. Raney
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Benedict Paten
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Parisa Nejad
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Brian T. Lee
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Katrina Learned
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Donna Karolchik
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Angie S. Hinrichs
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Steve Heitner
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Rachel A. Harte
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
2Invitae, San Francisco, CA 94017, USA
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Maximilian Haeussler
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Luvina Guruvadoo
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Pauline A. Fujita
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
3Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
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Christopher Eisenhart
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Mark Diekhans
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Hiram Clawson
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Jonathan Casper
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Galt P. Barber
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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David Haussler
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
4Howard Hughes Medical Institute, University of California Santa Cruz, CA 95064, USA
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Robert M. Kuhn
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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W. James Kent
1UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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ABSTRACT

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the “Data Integrator”, for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 17, 2015.
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The UCSC Genome Browser database: 2016 update
Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent
bioRxiv 027037; doi: https://doi.org/10.1101/027037
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The UCSC Genome Browser database: 2016 update
Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent
bioRxiv 027037; doi: https://doi.org/10.1101/027037

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