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Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2018 update. Nucleic Acids Res 2019; 46:D762-D769. [PMID: 29106570 PMCID: PMC5753355 DOI: 10.1093/nar/gkx1020] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/18/2017] [Indexed: 12/14/2022] Open
Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.
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Affiliation(s)
- Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chris Villarreal
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cath Tyner
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - David Gibson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ian T Fiddes
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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2
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Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 2017; 45:D626-D634. [PMID: 27899642 PMCID: PMC5210591 DOI: 10.1093/nar/gkw1134] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.
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Affiliation(s)
- Cath Tyner
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Clayton M Fischer
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Gibson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Luvina Guruvadoo
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Parisa Nejad
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chris Villarreal
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John Vivian
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res 2015; 44:D717-25. [PMID: 26590259 PMCID: PMC4702902 DOI: 10.1093/nar/gkv1275] [Citation(s) in RCA: 334] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/03/2015] [Indexed: 01/19/2023] Open
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.
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Affiliation(s)
- Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Parisa Nejad
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Maximilian Haeussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Pauline A Fujita
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA Howard Hughes Medical Institute, University of California Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AFA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res 2014; 43:D670-81. [PMID: 25428374 PMCID: PMC4383971 DOI: 10.1093/nar/gku1177] [Citation(s) in RCA: 690] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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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Affiliation(s)
- Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Timothy R Dreszer
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Pauline A Fujita
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rachel A Harte
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Glenn Hickey
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Robert Hubley
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Donna Karolchik
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Chin H Li
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ngan Nguyen
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | | | - Matthew L Speir
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 2014; 42:D764-70. [PMID: 24270787 PMCID: PMC3964947 DOI: 10.1093/nar/gkt1168] [Citation(s) in RCA: 550] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 12/17/2022] Open
Abstract
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 provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.
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Affiliation(s)
- Donna Karolchik
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Galt P. Barber
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Melissa S. Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Timothy R. Dreszer
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Pauline A. Fujita
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rachel A. Harte
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Angie S. Hinrichs
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian T. Lee
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Chin H. Li
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brian J. Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Brooke Rhead
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Kate R. Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Cricket A. Sloan
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Matthew L. Speir
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ann S. Zweig
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - W. James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
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6
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Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 2013; 41:D64-9. [PMID: 23155063 PMCID: PMC3531082 DOI: 10.1093/nar/gks1048] [Citation(s) in RCA: 612] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 10/08/2012] [Indexed: 11/14/2022] Open
Abstract
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 wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.
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Affiliation(s)
- Laurence R. Meyer
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Ann S. Zweig
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Angie S. Hinrichs
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Matthew Wong
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Cricket A. Sloan
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Kate R. Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Greg Roe
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Brooke Rhead
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Brian J. Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Andy Pohl
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Venkat S. Malladi
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Chin H. Li
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Brian T. Lee
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Vanessa Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Fan Hsu
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Rachel A. Harte
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Mary Goldman
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Belinda M. Giardine
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Pauline A. Fujita
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Timothy R. Dreszer
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Melissa S. Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Galt P. Barber
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - W. James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
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7
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Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, James Kent W. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012; 40:D918-23. [PMID: 22086951 PMCID: PMC3245018 DOI: 10.1093/nar/gkr1055] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/18/2011] [Accepted: 10/25/2011] [Indexed: 01/05/2023] Open
Abstract
The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced 'track data hubs', which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.
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Affiliation(s)
- Timothy R. Dreszer
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Ann S. Zweig
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Angie S. Hinrichs
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Brian J. Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Laurence R. Meyer
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Mathew Wong
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Cricket A. Sloan
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Kate R. Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Greg Roe
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Brooke Rhead
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Andy Pohl
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Venkat S. Malladi
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Chin H. Li
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Vanessa Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Fan Hsu
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Rachel A. Harte
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Luvina Guruvadoo
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Mary Goldman
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Belinda M. Giardine
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Pauline A. Fujita
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Melissa S. Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - Galt P. Barber
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
| | - W. James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Centre for Genomic Regulation (CRG), Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
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Abstract
Changes in the electrophoretic pattern were noted in the products of polypeptides of identical basic amino acids preincubated with reactive or degraded PN, suggesting the occurrence of N-nitrosation of the epsilon-amino group of lysine, the guanido group of arginine and the imidazole group of histidine. Additionally, increase in the N-nitroso immunoreactivity of preincubated histones H2A and H2B was detected by Western blot analysis.
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Affiliation(s)
- Wu-Nan Kuo
- Division of Science and Mathematics, Bethune-Cookman College, Daytona Beach, Florida 32114, USA.
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