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Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline M, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs A, Kuhn R, Lee B, Lee C, Le Mercier P, Miga K, Nassar L, Nejad P, Paten B, Perez G, Schmelter D, Speir M, Wick B, Zweig A, Haussler D, Kent W, Haeussler M. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res 2024; 52:D1082-D1088. [PMID: 37953330 PMCID: PMC10767968 DOI: 10.1093/nar/gkad987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.
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Affiliation(s)
- Brian J Raney
- 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
| | - Anna Benet-Pagès
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Medical Genetics Center (Medizinisch Genetisches Zentrum), Munich 80335, Germany
| | - 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
| | - Melissa S Cline
- 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 Fischer
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Glenn Hickey
- 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
| | | | - 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
| | - Phillipe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
| | - Karen H Miga
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luis R Nassar
- 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
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gerardo Perez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Daniel Schmelter
- 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
| | - Brittney D Wick
- 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
| | - W James Kent
- 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
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2
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Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M. GenArk: towards a million UCSC genome browsers. Genome Biol 2023; 24:217. [PMID: 37784172 PMCID: PMC10544498 DOI: 10.1186/s13059-023-03057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.
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Affiliation(s)
- Hiram Clawson
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA.
| | - Brian T Lee
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Clay Fischer
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | | | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Luis R Nassar
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Gerardo Perez
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Brittney Wick
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Daniel Schmelter
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Joel Armstrong
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
| | - W James Kent
- Genomics Institute, University of California, Santa Cruz, CA, 95064, USA
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3
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Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M. GenArk: Towards a million UCSC Genome Browsers. Res Sq 2023:rs.3.rs-2697398. [PMID: 37066427 PMCID: PMC10104252 DOI: 10.21203/rs.3.rs-2697398/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands of new genome assemblies have become available over the last decade, accessibility is limited by the work involved in manually creating browsers and curating annotations. The results can push the limits of data storage infrastructure. To facilitate managing this increasing number of genome assemblies, we created the Genome Archive (GenArk) collection of UCSC Genome Browsers from assemblies hosted at NCBI(1). Built on our established assembly hub system, this collection enables fast, on-demand visualization of chromosome regions without requiring a database server. Available annotations include gene models, some mapped through whole-genome alignments, repeat masks, GC content, and others. We also modified our popular BLAT(2) aligner and in-silico PCR to support a large number of genomes using limited RAM. Users can upload additional annotations themselves via track hubs(3) and custom tracks. We can import more annotations in bulk from third-party resources, demonstrated here with TOGA(4) gene models. 2,430 GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be found by searching on the main UCSC gateway page. We will continue to add human high-quality assemblies and for other organisms, we are looking forward to receiving requests from the research community for ever more browsers and whole-genome alignments via http://genome.ucsc.edu/assemblyRequest.html.
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Affiliation(s)
- Hiram Clawson
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Clay Fischer
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | | | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Luis R Nassar
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Gerardo Perez
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Brittney Wick
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel Schmelter
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Bogdan M. Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
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4
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Nair S, Barrett A, Li D, Raney BJ, Lee BT, Kerpedjiev P, Ramalingam V, Pampari A, Lekschas F, Wang T, Haeussler M, Kundaje A. The dynseq browser track shows context-specific features at nucleotide resolution. Nat Genet 2022; 54:1581-1583. [PMID: 36241719 PMCID: PMC10015500 DOI: 10.1038/s41588-022-01194-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-throughput experimental platforms have revolutionized the ability to profile biochemical and functional properties of biological sequences such as DNA, RNA and proteins. By collating several data modalities with customizable tracks rendered using intuitive visualizations, genome browsers enable an interactive and interpretable exploration of diverse types of genome profiling experiments and derived annotations. However, existing genome browser tracks are not well suited for intuitive visualization of high-resolution DNA sequence features such as transcription factor motifs. Typically, motif instances in regulatory DNA sequences are visualized as BED-based annotation tracks, which highlight the genomic coordinates of the motif instances but do not expose their specific sequences. Instead, a genome sequence track needs to be cross-referenced with the BED track to identify sequences of motif hits. Even so, quantitative information about the motif instances such as affinity or conservation as well as differences in base resolution from the consensus motif are not immediately apparent. This makes interpretation slow and challenging. This problem is compounded when analyzing several cellular states and/or molecular readouts (such as ATAC-seq and ChIP–seq) simultaneously, as coordinates of enriched regions (peaks) and the set of active transcription factor motifs vary across cell states.
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Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Daofeng Li
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Ting Wang
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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5
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Benet-Pagès A, Rosenbloom KR, Nassar LR, Lee CM, Raney BJ, Clawson H, Schmelter D, Casper J, Gonzalez JN, Perez G, Lee BT, Zweig AS, James Kent W, Haeussler M, Kuhn RM. Variant Interpretation: UCSC Genome Browser Recommended Track Sets. Hum Mutat 2022; 43:998-1011. [PMID: 35088925 PMCID: PMC9288501 DOI: 10.1002/humu.24335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 11/11/2022]
Abstract
The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anna Benet-Pagès
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Medical Genetics Center (MGZ), Munich, Germany
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Luis R Nassar
- 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 J Raney
- 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
| | - Daniel Schmelter
- 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
| | | | - Gerardo Perez
- 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
| | - Ann S Zweig
- 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
| | | | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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6
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Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. UCSC Cell Browser: Visualize Your Single-Cell Data. Bioinformatics 2021; 37:4578-4580. [PMID: 34244710 PMCID: PMC8652023 DOI: 10.1093/bioinformatics/btab503] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
Summary As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets. Availability and implementation We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Nikolay S Markov
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Pablo Moreno
- EMBL-EBI European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.,Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Irene Papatheodorou
- EMBL-EBI European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lucas Seninge
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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7
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Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, Clawson H, Casper J, Benet-Pagès A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 2021; 49:D1046-D1057. [PMID: 33221922 PMCID: PMC7779060 DOI: 10.1093/nar/gkaa1070] [Citation(s) in RCA: 273] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/19/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.
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Affiliation(s)
| | - Ann S Zweig
- 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
| | - Daniel Schmelter
- 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
| | - Conner C Powell
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luis R Nassar
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nathan D Maulding
- 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
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alastair C Fyfe
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jason D Fernandes
- 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
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anna Benet-Pagès
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Medical Genetics Center (MGZ), Munich, Germany
| | - 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, Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- 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
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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8
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Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M, Corbet-Detig R, Kent WJ, Haussler D, Haeussler M. The UCSC SARS-CoV-2 Genome Browser. Nat Genet 2020; 52:991-998. [PMID: 32908258 PMCID: PMC8016453 DOI: 10.1038/s41588-020-0700-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [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] [Indexed: 11/13/2022]
Abstract
Background: Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis. Results: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html ) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day. Conclusions: We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.
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Affiliation(s)
- Jason D Fernandes
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hiram Clawson
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Brian T Lee
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Luis R Nassar
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Brian J Raney
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Santrupti Nerli
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Arjun A Rao
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Schmelter
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alastair Fyfe
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nathan Maulding
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ann S Zweig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russ Corbet-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - W James Kent
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
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9
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Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ. UCSC Genome Browser enters 20th year. Nucleic Acids Res 2020; 48:D756-D761. [PMID: 31691824 PMCID: PMC7145642 DOI: 10.1093/nar/gkz1012] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 12/27/2022] Open
Abstract
The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a ‘lollipop’ plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.
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Affiliation(s)
- Christopher M Lee
- 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
| | | | - Angie S Hinrichs
- 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
| | - Luis R Nassar
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Conner C Powell
- 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
| | - Daniel Schmelter
- 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
| | - 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, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Genomics 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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10
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Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res 2020; 47:D853-D858. [PMID: 30407534 PMCID: PMC6323953 DOI: 10.1093/nar/gky1095] [Citation(s) in RCA: 505] [Impact Index Per Article: 126.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/19/2018] [Indexed: 01/17/2023] Open
Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.
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Affiliation(s)
- Maximilian Haeussler
- 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
| | - 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
| | - Angie S Hinrichs
- 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
| | - 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, 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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11
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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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12
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Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Res 2018; 28:1720-1732. [PMID: 30341161 PMCID: PMC6211643 DOI: 10.1101/gr.236273.118] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [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: 03/06/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
Abstract
Despite the rapid development of sequencing technologies, the assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout 2, a reference-assisted assembly tool that works for large and complex genomes. By taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout 2 infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. By using Ragout 2, we transformed NGS assemblies of 16 laboratory mouse strains into sets of complete chromosomes, leaving <5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long Pacific Biosciences (PacBio) reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. We applied Ragout 2 to the Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared with other genomes from the Muridae family. Chromosome painting maps confirmed most large-scale rearrangements that Ragout 2 detected. We applied Ragout 2 to improve draft sequences of three ape genomes that have recently been published. Ragout 2 transformed three sets of contigs (generated using PacBio reads only) into chromosome-scale assemblies with accuracy comparable to chromosome assemblies generated in the original study using BioNano maps, Hi-C, BAC clones, and FISH.
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Affiliation(s)
- Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Matthew Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Duncan Odom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham NG7 2NR, United Kingdom
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich NR4 7UG, United Kingdom
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Son Pham
- BioTuring Incorporated, San Diego, California 92121, USA
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13
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Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, Di Stefano L, Dinguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, FitzGerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, de Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, de Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TAL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ, Rast JP, Rollinson D, Rosse IC, Rotgans B, Routledge EJ, Ryan KM, Scholte LLS, Storey KB, Swain M, Tennessen JA, Tomlinson C, Trujillo DL, Volpi EV, Walker AJ, Wang T, Wannaporn I, Warren WC, Wu XJ, Yoshino TP, Yusuf M, Zhang SM, Zhao M, Wilson RK. Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nat Commun 2017; 8:16153. [PMID: 28832025 PMCID: PMC5569240 DOI: 10.1038/ncomms16153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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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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15
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Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics 2016; 32:1430-2. [PMID: 26740527 PMCID: PMC4848401 DOI: 10.1093/bioinformatics/btv766] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/28/2015] [Indexed: 01/29/2023] Open
Abstract
Summary: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores. Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. Contact: angie@soe.ucsc.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Brian J Raney
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Brooke Rhead
- Computational Biology Graduate Group, University of California, Berkeley, CA, USA and
| | - Jonathan Casper
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Donna Karolchik
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert M Kuhn
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Ann S Zweig
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA, USA, Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | - W James Kent
- Genomics Institute, University of California, Santa Cruz, CA, USA
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16
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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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17
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Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GWC, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 2015; 25:1921-33. [PMID: 26377836 PMCID: PMC4665013 DOI: 10.1101/gr.192922.115] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [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: 04/08/2015] [Accepted: 09/10/2015] [Indexed: 01/20/2023]
Abstract
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.
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Affiliation(s)
- Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Raquel García-Pérez
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Chad Tomlinson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mariano Rocchi
- Department of Biology, University of Bari, Bari 70126, Italy
| | | | - Oronzo Capozzi
- Department of Biology, University of Bari, Bari 70126, Italy
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Michael J Montague
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kim Kyung
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Milinn Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colby Chiang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | | | - Nam Tran
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yu Huang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yoon J Jung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Christopher A Schmitt
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Nikoleta Juretic
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | | | - Trudy R Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53705, USA; Department of Genetics Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9300 South Africa
| | - Roger W Wiseman
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jennifer J Tuscher
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Julie A Karl
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jörn E Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Roland Zahn
- Crucell Holland B.V., 2333 CN Leiden, The Netherlands
| | - David H O'Connor
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Eugene Redmond
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Alex Nisbett
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Béatrice Jacquelin
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France
| | | | - Jason M Brenchley
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA
| | | | | | | | - Jay R Kaplan
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Matthew J Jorgensen
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Brian J Raney
- University of California Santa Cruz, Santa Cruz, California 95060, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Juergen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany; Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Angela Noll
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50122 Florence, Italy
| | - David Webb
- National Center for Biotechnology Information, Bethesda, Maryland 20894, USA
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Tomas Marques-Bonet
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
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18
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Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet 2015; 47:272-5. [PMID: 25621460 DOI: 10.1038/ng.3198] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 12/29/2014] [Indexed: 12/13/2022]
Abstract
Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
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Affiliation(s)
- Andrew D Foote
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Gregg W C Thomas
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
| | - Tomáš Vinař
- Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Margaret E Hunter
- Sirenia Project, Southeast Ecological Science Center, US Geological Survey, Gainesville, Florida, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kerstin Lindblad-Toh
- 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annalaura Mancia
- 1] Marine Biomedicine and Environmental Science Center, Medical University of South Carolina, Charleston, South Carolina, USA. [2] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Rasmus Nielsen
- Center for Theoretical Evolutionary Genomics, University of California, Berkeley, Berkeley, California, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Nagarjun Vijay
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- 1] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew W Hahn
- 1] School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA. [2] Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
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19
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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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20
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Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ. The UCSC Ebola Genome Portal. PLoS Curr 2014; 6. [PMID: 25685613 PMCID: PMC4318873 DOI: 10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background:
With the Ebola epidemic raging out of control in West Africa, there has been a flurry of research into the Ebola virus, resulting in the generation of much genomic data.
Methods:
In response to the clear need for tools that integrate multiple strands of research around molecular sequences, we have created the University of California Santa Cruz (UCSC) Ebola Genome Browser, an adaptation of our popular UCSC Genome Browser web tool, which can be used to view the Ebola virus genome sequence from GenBank and nearly 30 annotation tracks generated by mapping external data to the reference sequence. Significant annotations include a multiple alignment comprising 102 Ebola genomes from the current outbreak, 56 from previous outbreaks, and 2 Marburg genomes as an outgroup; a gene track curated by NCBI; protein annotations curated by UniProt and antibody-binding epitopes curated by IEDB. We have extended the Genome Browser’s multiple alignment color-coding scheme to distinguish mutations resulting from non-synonymous coding changes, synonymous changes, or changes in untranslated regions.
Discussion:
Our Ebola Genome portal at http://genome.ucsc.edu/ebolaPortal/ links to the Ebola virus Genome Browser and an aggregate of useful information, including a collection of Ebola antibodies we are curating.
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Affiliation(s)
| | - Donna Karolchik
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Hiram Clawson
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Brian J Raney
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Kate R Rosenbloom
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Pauline A Fujita
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | | | - Chris Eisenhart
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - Ann S Zweig
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - David Haussler
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
| | - W James Kent
- CBSE, University of California Santa Cruz, Santa Cruz, California, USA
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21
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Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics 2014; 31:764-6. [PMID: 25348212 PMCID: PMC4341066 DOI: 10.1093/bioinformatics/btu712] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [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] [Indexed: 01/17/2023] Open
Abstract
Summary: Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Availability and implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). Contact:genome@soe.ucsc.edu
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Affiliation(s)
- Maximilian Haeussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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22
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Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Erratum: Corrigendum: Elephant shark genome provides unique insights into gnathostome evolution. Nature 2014. [DOI: 10.1038/nature13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Comparative assembly hubs: web-accessible browsers for comparative genomics. ACTA ACUST UNITED AC 2014; 30:3293-301. [PMID: 25138168 DOI: 10.1093/bioinformatics/btu534] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MOTIVATION Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers. RESULTS We introduce a pipeline to easily generate collections of Web-accessible UCSC Genome Browsers interrelated by an alignment. It is intended to democratize our comparative genomic browser resources, serving the broad and growing community of evolutionary genomicists and facilitating easy public sharing via the Internet. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications. To demonstrate this work, we create a comparative assembly hub containing 57 Escherichia coli and 9 Shigella genomes and show examples that highlight their unique biology. AVAILABILITY AND IMPLEMENTATION The source code is available as open source at: https://github.com/glennhickey/progressiveCactus The E.coli and Shigella genome hub is now a public hub listed on the UCSC browser public hubs Web page.
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Affiliation(s)
- Ngan Nguyen
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Glenn Hickey
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, 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 Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, 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 Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Ann Zweig
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - William James Kent
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, 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 Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, 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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24
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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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25
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Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 2013; 30:1003-5. [PMID: 24227676 PMCID: PMC3967101 DOI: 10.1093/bioinformatics/btt637] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
SUMMARY Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. AVAILABILITY AND IMPLEMENTATION Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.
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Affiliation(s)
- Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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26
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Bradley Shaffer H, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 2013; 14:R28. [PMID: 23537068 PMCID: PMC4054807 DOI: 10.1186/gb-2013-14-3-r28] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/15/2013] [Accepted: 03/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. RESULTS Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. CONCLUSIONS Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Daniel E Warren
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Andrew M Shedlock
- College of Charleston Biology Department and Grice Marine Laboratory, Charleston, SC 29424, USA
- Medical University of South Carolina College of Graduate Studies and Center for Marine Biomedicine and Environmental Sciences, Charleston, SC 29412, USA
| | - Robert C Thomson
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - John Abramyan
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101 USA
| | - Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Kyle K Biggar
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Glen M Borchert
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biological Sciences, Life Sciences Building, University of South Alabama, Mobile, AL 36688-0002, USA
| | | | - Rachel M Bowden
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leslie T Buck
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5, Canada
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mike Czerwinski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kim D Delehaunty
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tina A Graves
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard E Green
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Ramkumar Hariharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud P.O, Thiruvananthapuram, Kerala 695014, India
| | - Omar Hernandez
- FUDECI, Fundación para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturales. Av, Universidad, Bolsa a San Francisco, Palacio de Las Academias, Caracas, Venezuela
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Daniel Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredric J Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Cyriac Kandoth
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Lesheng Kong
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - AP Jason de Koning
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yang Li
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Lindsey Mork
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Ryan T Paitz
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Srihari Radhakrishnan
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Joy M Richman
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - John St John
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Tonia Schwartz
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Arun Sethuraman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Nay Thane
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia
| | - Laura M Zimmerman
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
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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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28
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St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012; 13:415. [PMID: 22293439 PMCID: PMC3334581 DOI: 10.1186/gb-2012-13-1-415] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
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29
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Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res 2012; 40:D912-7. [PMID: 22075998 PMCID: PMC3245183 DOI: 10.1093/nar/gkr1012] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [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: 10/20/2011] [Indexed: 11/23/2022] Open
Abstract
The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genome-preview.ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets.
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Affiliation(s)
- Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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30
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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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31
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Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science 2011; 333:1019-24. [PMID: 21852499 DOI: 10.1126/science.1202702] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
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Affiliation(s)
- Craig B Lowe
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
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32
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Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res 2010; 39:D871-5. [PMID: 21037257 PMCID: PMC3013645 DOI: 10.1093/nar/gkq1017] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [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] [Indexed: 01/19/2023] Open
Abstract
The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.
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Affiliation(s)
- Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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33
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Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2010; 39:D876-82. [PMID: 20959295 PMCID: PMC3242726 DOI: 10.1093/nar/gkq963] [Citation(s) in RCA: 841] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.
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Affiliation(s)
- Pauline A Fujita
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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34
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Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 2009; 38:D620-5. [PMID: 19920125 PMCID: PMC2808953 DOI: 10.1093/nar/gkp961] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access.
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Affiliation(s)
- Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA.
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35
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Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2009; 38:D613-9. [PMID: 19906737 PMCID: PMC2808870 DOI: 10.1093/nar/gkp939] [Citation(s) in RCA: 500] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data. As of September 2009, genomic sequence and a basic set of annotation ‘tracks’ are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
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Affiliation(s)
- Brooke Rhead
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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36
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Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol 2008; 15:1007-27. [PMID: 18774902 DOI: 10.1089/cmb.2008.0069] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.
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Affiliation(s)
- Jian Ma
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
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37
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Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2008; 37:D755-61. [PMID: 18996895 PMCID: PMC2686463 DOI: 10.1093/nar/gkn875] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [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] [Indexed: 11/12/2022] Open
Abstract
The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.
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Affiliation(s)
- R M Kuhn
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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38
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Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2007; 36:D773-9. [PMID: 18086701 PMCID: PMC2238835 DOI: 10.1093/nar/gkm966] [Citation(s) in RCA: 403] [Impact Index Per Article: 23.7] [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] [Indexed: 01/06/2023] Open
Abstract
The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.
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Affiliation(s)
- D Karolchik
- Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.
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39
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Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, Haussler D, Kent WJ. The ENCODE Project at UC Santa Cruz. Nucleic Acids Res 2007; 35:D663-7. [PMID: 17166863 PMCID: PMC1781110 DOI: 10.1093/nar/gkl1017] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 11/01/2006] [Accepted: 11/02/2006] [Indexed: 12/02/2022] Open
Abstract
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website (http://genome.ucsc.edu/ENCODE) is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples.
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Affiliation(s)
- Daryl J Thomas
- Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
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40
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Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ. The UCSC genome browser database: update 2007. Nucleic Acids Res 2006; 35:D668-73. [PMID: 17142222 PMCID: PMC1669757 DOI: 10.1093/nar/gkl928] [Citation(s) in RCA: 226] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at .
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Affiliation(s)
- R M Kuhn
- Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.
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41
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Abstract
This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. We identify 3171 intervals, covering approximately 92% of the human genome, within which we find no rearrangements larger than 50 kilobases (kb) in the lineages leading to human, mouse, rat, and dog from their most recent common ancestor. Combining intervals that are adjacent in all contemporary species produces 1338 segments that may contain large insertions or deletions but that are free of chromosome fissions or fusions as well as inversions or translocations >50 kb in length. We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals.
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Affiliation(s)
- Jian Ma
- Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.
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42
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Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006; 34:D590-8. [PMID: 16381938 PMCID: PMC1347506 DOI: 10.1093/nar/gkj144] [Citation(s) in RCA: 847] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .
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Affiliation(s)
- A S Hinrichs
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.
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