UCSC Genome Browser Acknowledgments
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The data and software displayed on this site are the result of
a large collaborative effort among many individuals at UCSC and
at research institutions around the world. We'd like to
acknowledge the scientists and engineers who have contributed
to the UCSC Genome Browser and its data, and the organizations
who have made this project possible through their generous
funding.
Mammals
Other Vertebrates
Deuterostomes
Insects
Nematodes
Other
Viruses
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Human Genome Browser: Acknowledgments
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The UCSC Human Genome Browser is generated by the
UCSC Genome Bioinformatics Group in
collaboration with the International Human Genome Project.
The browser project is funded by grants from the
National Human Genome Research Institute,
and generous support from the
Howard Hughes Medical Institute and the
California Institutes for Science and Innovation.
We work with collaborators at many other institutions
to produce and annotate this reference sequence of the human genome.
To view complete acknowledgments for a specific annotation, see the
"Credits" section on the track's description page
in the Genome Browser. For a list of browser-related publications,
see our publications page.
UCSC Human Genome Browsers:
- hg38 (GRCh38):
Hiram Clawson, Brian Raney, Robert Kuhn, Donna Karolchik, Steve Heitner
- hg19 (GRCh37): Hiram Clawson, Brooke Rhead,
Pauline Fujita, Ann Zweig, Katrina Learned, Donna Karolchik and Robert Kuhn
- hg18:
Engineering effort led by Fan Hsu; QA effort led by Ann Zweig
- hg17:
Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik,
Kate Rosenbloom, Angie Hinrichs, Rachel Harte, and Jim Kent
- hg16:
Terry Furey, Hiram Clawson,
Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent
- hg15 (archived): Jim Kent, Terry Furey, Matt Schwartz,
Heather Trumbower, Angie Hinrichs, Fan Hsu, Donna Karolchik, Jorge Garcia,
Patrick Gavin, Chuck Sugnet, Yontao Lu, Mark Diekhans, Ryan Weber,
Robert Baertsch, Krishna Roskin, and many other students in the UCSC
Genome Bioinformatics group
- Earlier browsers (archived): UCSC Genome Bioinformatics staff and
students
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Human Genome: Data Sources
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Starting with the hg19 (GRCh37) assembly, the human genome sequence is
provided by
the Genome Reference Consortium (GRC), whose goal is to correct
the small number of regions in the reference that are currently misrepresented,
to close as many remaining gaps as possible and to produce alternative
assemblies of structurally variant loci when necessary.
Prior to hg19, the
human genome sequence data used by the browser were generated by laboratories
belonging to the Human Genome Sequencing Consortium.
Periodic freezes of this data were generated by
NCBI, and EST, mRNA,
BACend and other types of data used for the assembly and annotation were
obtained from GenBank, European Molecular Biology Lab (EMBL), and
DNA Data Bank of Japan (DDBJ).
Clone maps were created by the individual sequencing centers.
The original chromosome files were produced by the institutions and
individuals listed in the table below.
Finished Chromosomes |
Chr. # |
Sequencing Centers |
AGP File |
1 |
The Sanger Institute, Cambridge, UK
University of Washington, Department of Genome Sciences,
Seattle, WA, USA
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Jane Rogers |
2 |
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
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Rick Wilson |
3 |
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
Beijing Genomics Institute/Human Genome Center,
Beijing, China
University of Washington, Department of Genome Sciences,
Seattle, WA, USA
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Steve Scherer |
4 |
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
Stanford Human Genome Center, Palo Alto, CA, USA
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Rick Wilson |
5 |
Joint Genome Institute,
U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA
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Jeremy Schmutz |
6 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
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Jane Rogers |
7 |
The Genome Institute at Washington University (WUSTL),
St. Louis, MO USA
University of Washington, Department of Genome Sciences,
Seattle, WA, USA
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Rick Wilson |
8 |
The Broad Institute, Cambridge, MA USA
Keio University, Tokyo, Japan
Institute of Molecular Biology (IMB),
Jena, Germany
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Chad Nusbaum |
9 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
Gesellschaft fuer Biotechnologische Forschung (GBF),
Braunschweig, Germany
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Jane Rogers |
10 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
Genome Therapeutics Corporation (GTC), Waltham, MA, USA
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Jane Rogers |
11 |
RIKEN Human Genome Research Group, Japan
The Broad Institute, Cambridge, MA USA
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Todd Taylor |
12 |
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
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Steve Scherer |
13 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
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Jane Rogers |
14 |
Genoscope National Sequencing Centre,
Evry, France
Institute for Systems Biology (ISB),
Seattle, WA
The Genome Institute at Washington University (WUSTL),
St. Louis, MO USA
RIKEN Human Genome Research Group, Japan
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Jean Weissenbach |
15 |
The Broad Institute, Cambridge, MA USA
Institute of Molecular Biology (IMB),
Institute for Systems Biology (ISB),
Seattle, WA
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Chad Nusbaum |
16 |
Joint Genome Institute (JGI),
U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA
The Institute for Genomic Research (TIGR),
Rockville, MD, USA
The Wellcome Trust Sanger Institute,
Cambridge, UK
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Jeremy Schmutz |
17 |
The Broad Institute, Cambridge, MA USA
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Chad Nusbaum |
18 |
The Broad Institute, Cambridge, MA USA
RIKEN Human Genome Research Group, Japan
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Chad Nusbaum |
19 |
Joint Genome Institute (JGI),
U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA
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Jeremy Schmutz |
20 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
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James Gilbert |
21 |
RIKEN Human Genome Research Group, Japan
Max Planck Institute for Molecular Genetics,
Berlin, Germany
Gesellschaft fuer Biotechnologische Forschung (GBF),
Braunschweig, Germany
Keio University School of Medicine,
Tokyo, Japan
Chromosome 21 Consortium
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Todd Taylor |
22 |
The Wellcome Trust Sanger Institute,
Cambridge, UK
The University of Oklahoma,
Norman, OK USA
Keio University School of Medicine,
Tokyo, Japan
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Jane Rogers |
X |
The Wellcome Trust Sanger Institute,
Cambridge, UK
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
Institute of Molecular Biology (IMB),
Jena, Germany
The Genome Institute at Washington University (WUSTL),
St. Louis, MO USA
Max Planck Institute for Molecular Genetics,
Berlin, Germany
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Jane Rogers |
Y |
The Genome Institute at Washington University (WUSTL),
St. Louis, MO USA
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Rick Wilson |
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The Alpaca Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC Alpaca Genome Browser/Initial Annotations:
- vicPac2:
Hiram Clawson and Luvina Guruvadoo
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vicPac1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The alpaca sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The alpaca data are provided with the following understanding:
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The data may be freely downloaded, used in analyses, and
repackaged in databases.
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Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
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Any redistribution of the data should carry this notice.
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The Armadillo Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC Armadillo Genome Browser/Initial Annotations:
- dasNov3:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The armadillo sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The armadillo data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
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Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
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Any redistribution of the data should carry this notice.
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The Baboon Genome Browser is provided by the Baboon Genome Sequencing Consortium
with the following acknowledgments:
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Funding:
National Human Genome Research Institute
(NHGRI), USA
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Sequencing/Assembly:
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
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UCSC Baboon Genome Browser/Initial Annotations:
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papAnu2:
Chin Li and Luvina Guruvadoo
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papHam1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The baboon sequence is made freely available for public use by the
Baboon Genome Sequencing Consortium. Please review the BCM-HGSC
conditions for use guidelines before using this data.
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The Bison Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
University of Maryland, College Park, MD, USA
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UCSC Bison Genome Browser/Initial Annotations:
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bisBis1:
Hiram Clawson and Chris Villarreal
The bison sequence is made freely available by the University of Maryland Genome
Assembly Group, Aleksey Zimin.
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The Bonobo Genome Browser is provided with the following acknowledgments:
The bonobo sequence is made freely available by the Max-Planck Institute for
Evolutionary Anthropology. The initial analysis of this dataset can be found in
Prüfer K et al.
The bonobo genome compared with the chimpanzee and human
genomes. Nature. 2012 Jun 28;486(7404):527-31.
PMID: 22722832
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The Bushbaby Genome Browser is provided with the following acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC Bushbaby Genome Browser/Initial Annotations:
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otoGar3:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The bushbaby sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The bushbaby data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
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Any redistribution of the data should carry this notice.
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The UCSC felCat8 Genome Browser displays data from the
Nov. 2014 Felis_catus_8.0 assembly of the domestic cat produced by the
International Cat Genome Sequencing Consortium. This assembly was provided
with the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI),
Bethesda, MD
- 454 Production sequencing:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
- BAC sequencing: The Genome Institute at WUSTL
- Plasmid and fosmid sequencing:
The Broad Institute,
Cambridge, MA, USA and Agencourt Bioscience
- Sequence assembly and data integration for creation of chromosomal
AGP files: The Genome Institute at WUSTL
- Cat RH map: Bill Murphy, Texas A&M University, College Station, TX.
- DNA source: Dr. Kristina Narfstrom,
University of Missouri, Columbia, MO.
- UCSC Cat Genome Browser/Initial Annotations (felCat8):
UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA -
Hiram Clawson, Brian Raney, and Christopher Lee
The UCSC felCat5 Genome Browser displays data from the
Sep. 2011 Felis_catus-6.2 assembly of the domestic cat produced by the
International Cat Genome Sequencing Consortium. This assembly was provided
with the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI),
Bethesda, MD
- 454 Production sequencing:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
- BAC sequencing: The Genome Institute at WUSTL
- Plasmid and fosmid sequencing:
The Broad Institute,
Cambridge, MA, USA and Agencourt Bioscience
- Sequence assembly and data integration for creation of chromosomal
AGP files: The Genome Institute at WUSTL
- Whole genome alignments: Brian Raney,
UCSC Genome Browser Group, University of
California, Santa Cruz, CA, and The Genome Institute at WUSTL
- Cat RH map: Bill Murphy, Texas A&M University, College Station, TX.
- DNA source: Dr. Kristina Narfstrom,
University of Missouri, Columbia, MO.
- UCSC Cat Genome Browser/Initial Annotations (felCat5):
UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA -
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo,
Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The UCSC felCat4
Genome Browser displays data from the
Dec. 2008 catChrV17e draft assembly, based on sequence
reads from six domestic cats and one wild cat. The
browser is provided with the following acknowledgments:
- Sequencing/Assembly:
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NHGRI Genome Technology Branch and NIH
Intramural Sequencing Center, Bethesda,
MD, USA
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Agencourt Bioscience,
Danvers, MA, USA
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NCI Laboratory of Genomic Diversity,
Frederick, MD, USA
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Hill's Pet Nutrition, Inc.,
Topeka, KS, USA
- UCSC Cat Genome Browser/Initial Annotations
(felCat4):
UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA -
Chin Li, Hiram Clawson, Antonio Coelho, Mary
Goldman, and Donna Karolchik
The UCSC felCat3
Genome Browser displays data from the
March 2006 v3 draft assembly of the domestic cat (Felis catus).
This assembly was provided with the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI),
Bethesda, MD
- Project Leadership:
The Broad Institute, Cambridge, MA, USA
- Sequencing/Assembly:
The Broad Institute - team led by by Kerstin Lindblad-Toh, Ph.D.
- Plasmid and fosmid libraries: The Broad Institute
- BAC end sequencing:
Agencourt Bioscience, Danvers, MA, USA
- UCSC Cat Genome Browser/Initial Annotations (felCat3):
UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA -
Heather Trumbower, Angie Hinrichs, Mark Diekhans,
Brooke Rhead, and Archana Thakkapallayil
The catChrV17e cat assembly was initially published in
Pontius JU et al.
Initial sequence and comparative analysis of the cat genome.
Genome Res. 2007 Nov;17(11):1675-89.
PMID: 17975172;
PMCID: PMC2045150
The Broad Institute released the initial 2X (v3) assembly of the cat genome as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The cat sequence is made freely available with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The UCSC Chimpanzee Genome Browsers display draft assembly
data produced by the Chimpanzee Genome Sequencing
Consortium:
- May 2016 panTro5 browser: v3.0 6x Sanger; 55x Illumina; 9x PacBio
- Feb. 2011 panTro4 browser: v2.1.4
chromosome-based 6X draft assembly
- Oct. 2010 panTro3 browser: v2.1.3
chromosome-based 6X draft assembly
- Mar. 2006 panTro2 browser: v2.1 chromosome-based
6X draft assembly (Oct. 2005)
- Nov. 2003 panTro1 browser: v1.1 Arachne draft assembly
The Chimpanzee Genome Browsers have the following acknowledgments:
- Funding: National Human Genome Research Institute
(NHGRI)
- Sequencing/Assembly (panTro5):
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BAC sequencing - McDonnell Genome Institute at Washington University School of
Medicine, St Louis, MO. Sequence generation.
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Assembly and data integration for creation of chromosomal AGP files:
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Lukas Kuderna and Tomas Marques-Bonet, ICREA at Institut de Biologia
Evolutiva, (UPF-CSIC), PRBB, 08003 Barcelona, Spain, and LaDeana Hillier,
McDonnell Genome Institute at Washington University School of Medicine, St.
Louis, MO.
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Wes Warren, Lars Feuk (Uppsala U), Andrew Sharp (Mt Sinai), Ed Green
(Dovetail), Mikkel Schierup (Aarhus U), and Bojan Obradovic (Illumina).
- Sequencing/Assembly (panTro2, panTro3, panTro4):
- Sequencing/Assembly (panTro1):
Sequence assembled by teams led by Eric
Lander, Ph.D. at The Broad Institute and Richard K. Wilson,
Ph.D. at The Genome Institute at WUSTL
- Alignments:
LaDeana Hillier, The Genome Institute at WUSTL and The Broad Institute
- Annotations:
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The Genome Institute at WUSTL, St. Louis, MO, USA
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Research Group on Biomedical Informatics of IMIM/UPF (GRIB),
Barcelona, Spain
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Riken Genomic Sciences Center, Yokohama City, Japan
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UCSC Genome Bioinformatics Group,
Santa Cruz, CA, USA
- UCSC Chimp Genome Browser:
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panTro5:
Hiram Clawson and Chris Villarreal.
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panTro4:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
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panTro3:
Hiram Clawson, Greg Roe, and Donna Karolchik
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panTro2:
Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana
Thakkapallayil, and Donna Karolchik
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panTro1:
Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert Kuhn, and
Donna Karolchik
The initial sequencing and analysis of the chimpanzee genome was published by the
Chimpanzee Sequencing and Analysis Consortium. The chimpanzee sequence data may be
freely downloaded, used in analyses, and repackaged in databases if the provider is
properly acknowledged. Please cite this publication when using these data:
The Chimpanzee Sequencing and Analysis Consortium.
Initial sequence of the chimpanzee genome and comparison with the
human genome. Nature. 2005 Sep 1;437(7055):69-87.
PMID: 16136131
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The Chinese pangolin assembly was submitted by Washington University (WashU) with
the following acknowledgments:
The Chinese pangolin sequence data may be freely downloaded, used in analyses,
and repackaged in databases if the provider is properly acknowledged: Dr. Richard
K. Wilson and The Genome Institute, Washington University School of Medicine.
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The UCSC Cow Genome Browser displays two different
assemblies of the bovine genome: one provided by the
University of Maryland Center for Bioinformatics and
Computational Biology (UMD CBCB) and one from the Baylor
College of Medicine Human Genome Sequencing Center (BCM-HGSC).
The assemblies available in the browser include:
- Jun. 2014 (bosTau8) assembly - UMD CBCB version UMD_3.1.1
- Oct. 2011 (bosTau7) assembly - Bovine Genome Sequencing Consortium
(BCM-HGSC) version Btau_4.6.1
- Nov. 2009 (bosTau6) assembly - UMD CBCB version UMD_3.1
- Oct. 2007 (bosTau4) assembly - BCM-HGSC version Btau_4.0
- Aug. 2006 (bosTau3) assembly - BCM-HGSC version Btau_3.1
- Mar. 2005 (bosTau2) assembly - BCM-HGSC version Btau_2.0
- Sep. 2004 (bosTau1) assembly - BCM-HGSC version Btau_1.0
The UMD CBCB genome assemblies are provided with the following acknowledgments:
The BCM-HGSC genome assemblies are provided with the following acknowledgments:
- Funding - For a list of the many agencies that
funded the cow sequencing project, see the BCM-HGSC
Bovine Genome Project page.
- BAC library DNA:
Dr. Michael MacNeil's laboratory at the
USDA Agricultural Research Service,
Miles City, MT, USA
- Whole genome shotgun sequence DNA:
Dr. Timothy Smith's laboratory at the
U.S. Meat Animal Research Center,
Clay Center, NE, USA
- BAC-based fingerprint map:
Genome Sciences Centre, Vancouver,
B.C.
- UCSC Cow Genome Browser/Initial Annotations:
- bosTau7:
Chin Li, Hiram Clawson, Brian Raney and Steve Heitner
- bosTau4:
Hiram Clawson, Brian Raney, and Ann Zweig
- bosTau3:
Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik
- bosTau2:
Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna
Karolchik
- bosTau1 (archived):
Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney,
Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik
The cow sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged. Please cite
the appropriate publication when using these data.
UMD cow assembly:
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F,
Pertea G, Van Tassell CP, Sonstegard TS et al.
A whole-genome assembly of the domestic cow, Bos taurus.
Genome Biol. 2009;10(4):R42.
Baylor cow assembly:
Bovine Genome Sequencing and Analysis Consortium.
The genome sequence of taurine cattle: a window to ruminant
biology and evolution.
Science. 2009 Apr 24;324(5926):522-8.
For more information see the
UMD CBCB
and the BCM-HGSC
Bovine Genome Project pages.
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Crab-eating Macaque Genome
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The Crab-eating Macaque Genome Browser is provided with the following
acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI)
- DNA source:
Dr. Jay Kaplan, Wake Forest Primate Facility, Wake Forest, NC
- Genome Sequence:
Genome Institute at Washington University (WUSTL), St.
Louis, MO, USA
- Sequence Assembly:
Richa Agarwala, Sergey Shiryaev, NCBI and The Genome Institute, Washington
University School of Medicine, St. Louis, MO, USA
- Assembly curation:
LaDeana Hillier, Genome Institute, Washington University School of Medicine,
St. Louis, MO, USA
- FISH mapping data:
Mariano Rocchi, Department of Biology, University of Bari, Bari, Italy
-
UCSC Crab-eating Macaque Genome Browser/Initial Annotations:
- macFas5:
Hiram Clawson, Brian Raney and Steve Heitner
The crab-eating macaque data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The UCSC Dog Genome Browser displays assemblies of the domestic dog
(Canis familiaris) with the following acknowledgments:
- Funding: The
National Human Genome Research Institute
- Project Leadership:
The Broad Institute, Cambridge, MA, USA
- Sequencing/Assembly:
The Broad Institute -
team led by by Kerstin Lindblad-Toh, Ph.D.
- Plasmid and fosmid libraries:
The Broad Institute
- BAC libraries:
Children's Hospital Oakland Research Institute
(CHORI), Oakland, CA, USA
- BAC end sequencing:
Agencourt Bioscience, Danvers, MA, USA
- RH map:
Centre National de la Recherche Scientifique
(CNRS), France
- FISH mapping: North Carolina State University (NCSU),
Raleigh, NC, USA
- Dog Selection:
Fred Hutchinson Cancer Research Center
(FHCRC), Seattle, WA, USA
- UCSC Dog Genome Browser/Initial Annotations:
- canFam3: Hiram Clawson and Luvina Guruvadoo
- canFam2: Angie Hinrichs, Jennifer Jackson, and Donna
Karolchik
- canFam1: Angie Hinrichs, Robert Kuhn and Donna
Karolchik
The dog genome sequence is made freely available by the
Dog Genome Sequencing Project.
Please cite this publication when using these data:
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M,
Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC et al.
Genome sequence, comparative analysis and haplotype structure
of the domestic dog.
Nature. 2005 Dec 8;438(7069):803-19. PMID: 16341006
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The Dolphin Genome Browser is provided with the following acknowledgments:
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Sequencing:
Baylor College of Medicine Human Genome Sequencing Center
(BCM-HGSC), Houston, TX, USA
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Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC Dolphin Genome Browser/Initial Annotations:
- turTru2: Hiram Clawson, Chin Li, Brian Raney, Pauline
Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna
Karolchik
The dolphin sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using
29 mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The dolphin data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The elephant assembly was provided by the Broad Institute with the following
acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Elephant Genome Browser/Initial Annotations:
- loxAfr3: Hiram Clawson, Pauline Fujita, Vanessa Swing,
Antonio Coelho, and Donna Karolchik
The elephant sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The ferret assembly was provided by the Ferret
Genome Sequencing Consortium with the following acknowledgments:
The ferret sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged. Please cite
this publication when using these data:
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D,
Law GL, Skunca N, Hatta M et al.
The draft genome sequence of the ferret (Mustela putorius furo)
facilitates study of human respiratory disease.
Nat Biotechnol. 2014 Dec;32(12):1250-5.
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The UCSC Gibbon Genome Browser displays data from the
draft assemblies of the northern white-cheeked gibbon
(Nomascus leucogenys) provided by the Gibbon Genome Sequencing
Consortium with the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
- UCSC Gibbon Genome Browser/Initial Annotations:
- nomLeu3: Pauline Fujita and Hiram Clawson
- nomLeu2: Hiram Clawson, Chin Li, Brian Raney, Pauline
Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna
Karolchik
- nomLeu1: Chin Li, Brooke Rhead, Steve Heitner, Lauren
Scott and Donna Karolchik
The gibbon sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged. Please cite
this publication when using these data:
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J,
Meyer TJ, Herrero J, Roos C, Aken B et al.
Gibbon genome and the fast karyotype evolution of small
apes.
Nature. 2014 Sep 11;513(7517):195-201.
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Golden Snub-Nosed Monkey Genome
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The golden snub-nosed monkey assembly (Rhinopithecus roxellana) is provided with
the following acknowledgments:
- Sequencing/Assembly:
Novogene
- UCSC Golden Snub-Nosed Monkey Genome Browser/Initial Annotations:
-
rhiRox1: Hiram Clawson, Luvina Guruvadoo
The golden snub-nosed monkey sequence data may be freely downloaded, used in
analyses, and repackaged in databases if the provider is properly acknowledged.
Please cite this publication when using these data:
Zhou X, Wang B, Pan Q, Zhang J, Kumar S, Sun X, Liu Z, Pan H, Lin Y, Liu G
et al.
Whole-genome sequencing of the snub-nosed monkey provides insights
into folivory and evolutionary history.
Nat Genet. 2014 Dec;46(12):1303-10.
PMID: 25362486
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The UCSC gorGor5
Genome Browser displays data from the Mar 2016 assembly of
Gorilla gorilla gorilla produced by the University of Washington.
This assembly is provided with the following acknowledgements:
- Sequencing/Assembly:
University of Washington
- UCSC Gorilla Genome Browser/Initial Annotations:
- gorGor5: Hiram Clawson and Jairo Navarro
The UCSC gorGor4
Genome Browser displays data from the Dec 2014 assembly of
Gorilla gorilla gorilla produced by the Wellcome Trust Sanger Institute.
This assembly is provided with the following acknowledgements:
- Sequencing/Assembly:
The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- UCSC Gorilla Genome Browser/Initial Annotations:
- gorGor4: Jonathan Casper, Brian Raney, Christopher Lee
The UCSC gorGor3
Genome Browser displays data from the May 2011 draft assembly
of Gorilla gorilla gorilla. This assembly is provided with
the following acknowledgments:
- Sequencing:
The Wellcome Trust Sanger Institute,
Hinxton, Cambridge, UK
- Assembly:
- UCSC Gorilla Genome Browser/Initial Annotations:
- gorGor3: Hiram Clawson, Mark Diekhans, Brian Raney,
Brooke Rhead, Steve Heitner, Lauren Scott and Donna Karolchik
The gorilla sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged. Please cite
this publication when using these data:
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A,
Lappalainen T, Mailund T, Marques-Bonet T et al.
Insights into hominid evolution from the gorilla genome
sequence.
Nature. 2012 Mar 7;483(7388):169-75.
PMID: 22398555;
PMCID: PMC3303130
Additionally, this publication discusses the gorGor5 assembly:
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M,
Raja A, Fiddes I, Hillier LW et al.
Long-read sequence assembly of the gorilla genome.
Science. 2016 Apr 1;352(6281):aae0344.
PMID: 27034376;
PMCID: PMC4920363
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The green monkey assembly (Chlorocebus sabeaus) is provided by the
Vervet Genomics Consortium with the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI)
- DNA source:
Dr. Jay Kaplan, Wake Forest Primate Facility, Wake Forest, NC, USA
- Genome Sequence:
- BAC Library:
Dr. Pieter DeJong, CHORI,
Oakland, CA, USA
- Assembly Curation:
- FISH Mapping Data:
Mariano Rocchi, Department of Biology, University of Bari, Bari, Italy
- cDNA data - RNA sources:
Dr. Nelson Freimer - Semel Institute for Neuroscience and Human Behavior,
University of California Los Angeles, CA, USA
- UCSC Green Monkey Genome Browser/Initial Annotations:
-
chlSab2: Hiram Clawson, Brian Raney, Christopher Lee
The green monkey sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The guinea pig assembly (Cavia porcellus) is provided with
the following acknowledgments:
The guinea pig sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The Hedgehog Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute at MIT and Harvard, Cambridge, MA, USA
- DNA Samples:
Dr. Neil J. Gemmell -
Reproduction, Genomics and Development Group, University of
Otago, Dunedin, New Zealand
-
UCSC Hedgehog Genome Browser/Initial Annotations:
-
eriEur2:
Hiram Clawson, Brian Raney and Steve Heitner
-
eriEur1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The hedgehog sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using
29 mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The hedgehog data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The UCSC Horse Genome Browser displays the draft assembly
of the horse (Equus caballus) genome from The
Broad Institute. This assembly is provided with the
following acknowledgments:
- Funding: The
National Human Genome Research Institute
- Project Leadership:
The Broad Institute, Cambridge, MA, USA
- Sequencing/Assembly:
The Broad Institute
- BAC End Reads:
University of Veterinary Medicine
Hanover, Germany, and the
Helmholtz Centre for Infection
Research, Braunschweig, Germany
- UCSC Horse Genome Browser/Initial Annotations:
-
equCab2:
Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna
Karolchik
-
equCab1:
Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate
Rosenbloom, and Donna Karolchik
The horse sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged. Please cite
this publication when using these data:
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL,
Adelson DL, Bailey E, Bellone RR et al.
Genome sequence, comparative analysis, and population genetics
of the domestic horse.
Science. 2009 Nov 6;326(5954):865-7.
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The Kangaroo Rat Genome Browser is provided with the
following acknowledgments:
- Sequencing:
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
- Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Kangaroo Rat Genome Browser/Initial Annotations:
-
dipOrd1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The kangaroo rat sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using
29 mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The kangaroo rat data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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Malayan Flying Lemur Genome
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The Malayan Flying lemur Genome Browser is provided with the
following acknowledgments:
The Malayan flying lemur sequence may be freely downloaded,
used in analyses, and repackaged in databases if the data
provider is properly acknowledged: Richard K. Wilson and The Genome Institute,
Washington University School of Medicine.
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The Manatee Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Manatee Genome Browser/Initial Annotations:
-
triMan1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The manatee sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged.
Please cite this publication when using these data:
Foote AD, Liu Y, Thomas GW, Vinař T, Alföldi, Deng J, Dugan S, van Elk
CE, Hunter ME, Joshi V et al.
Convergent evolution of the genomes of marine mammals.
Nat Genet. 2015 Mar;47(3):272-5.
PMID: 25621460;
PMCID: PMC4644735
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The Marmoset Genome Browser is provided with the following acknowledgments:
-
Sequencing and assembly:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA and
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA
-
DNA Source:
Dr. Suzette Tardif,
Southwest National Primate Research Center,
San Antonio, TX, USA
-
CHORI-259 BAC library:
Dr. Pieter DeJong,
Children's Hospital Oakland Research Institute,
Oakland, CA, USA
-
UCSC Marmoset Genome Browser/Initial Annotations:
-
calJac3:
Hiram Clawson, Chin Li, Mark Diekhans, Mary Goldman, Vanessa Swing, and
Donna Karolchik
-
calJac1:
Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna
Karolchik
These data were produced by The Genome Institute at WUSTL and the BCM-HGSC
and can be downloaded
here.
The marmoset sequence data may be freely downloaded, used in analyses, and
repackaged in databases if the provider is properly acknowledged.
Please cite this publication when using these data:
Marmoset Genome Sequencing and Analysis Consortium.
The common marmoset genome provides insight into primate biology and
evolution.
Nat Genet. 2014 Aug;46(8):850-7.
PMID: 25038751;
PMCID: PMC4138798
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The Megabat (Fruitbat) Genome Browser is provided with the following
acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
-
UCSC Megabat Genome Browser/Initial Annotations:
-
pteVam1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The megabat sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The megabat data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The microbat (little brown bat) genome is provided by
The Broad Institute with the following acknowledgments:
-
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
-
UCSC Microbat Genome Browser/Initial Annotations:
-
myoLuc2:
Chin Li, Brian Raney, Robert Kuhn, Steve Heitner, Brooke Rhead, Greg Roe and
Donna Karolchik
The microbat sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The microbat data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The minke whale genome is provided by the Korea Institute of Ocean Science and
Technology with the following acknowledgments:
The minke whale genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC,
Kwon KK et al.
Minke whale genome and aquatic adaptation in cetaceans.
Nat Genet. 2014 Jan;46(1):88-92.
PMID: 24270359
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Starting with mm10
(GRCm38), the mouse genome assembly is now provided by the
Genome Reference Consortium (GRC). See the
GRC Mouse Genome web pages for acknowledgments.
Prior to mm10/GRCm38, mouse assemblies were produced by the Mouse Genome
Sequencing Consortium, with these acknowledgments:
- Funding:
- Sequencing:
- Physical Map:
- Assembly: Deanna Church, Richa Agarwala, Josh
Cherry, Mike DiCuccio, Hsiu-Chuan Chen, Paul Kitts,
Victor Sapojnikov
- cDNA Sequencing:
- UCSC Mouse Genome Browser:
-
mm10:
Hiram Clawson and Luvina Guruvadoo
-
mm9:
Hiram Clawson, Archana Thakkapallayil, Robert Kuhn and Donna Karolchik
-
mm8:
Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead,
Archana Thakkapallayil, and Donna Karolchik
-
mm7:
Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik
-
mm6 (archived): Hiram Clawson, Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali
Sultan-Qurraie, Heather Trumbower and Donna Karolchik
- Annotations:
The initial 3X coverage of the mouse genome was produced by
the Mouse Sequencing Consortium, with the following acknowledgments:
- Project Oversight: Arthur Holden and Francis Collins
- Funding:
- Sequencing:
The mouse genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse genome.
Nature. 2002 Dec 5;420(6915):520-62.
PMID: 12466850
For more information about mouse assemblies provided by the GRC, see the
GRC mouse genome web pages. For information about assemblies
prior to mm10/GRCm38, see the Wellcome Trust Sanger Institute
Mouse Resource Portal.
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The Mouse Lemur Genome Browser is provided with the following acknowledgments:
- Sequencing/Assembly:
-
UCSC Mouse Lemur Genome Browser/Initial Annotations:
-
micMur2:
Hiram Clawson, Brian Raney, Christopher Lee
-
micMur1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The mouse lemur sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The mouse lemur data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The naked mole-rat genome was provided with the following acknowledgments:
-
Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China
-
UCSC Naked Mole-rat Genome Browser/Initial Annotations:
-
hetGla2:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
-
hetGla1:
Chin Li and Luvina Guruvadoo
The naked mole-rat genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V,
Di Palma F, Lindblad-Toh K, Church GM et al.
The Naked Mole Rat Genome Resource: facilitating analyses of
cancer and longevity-related adaptations.
Bioinformatics. 2014 Dec 15;30(24):3558-60.
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The opossum genome assembly (Monodelphis domestica) is provided
by The Broad Institute with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute,
Cambridge, MA, USA
- FISH Mapping:
North
Carolina State University (NCSU), Raleigh, NC, USA
- UCSC Opossum Genome Browser/Initial Annotations:
-
monDom5:
Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and
Katrina Learned
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monDom4:
Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna
Karolchik
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monDom1:
Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna
Karolchik
The opossum genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M,
Gentles AJ, Goodstadt L, Heger A et al.
Genome of the marsupial Monodelphis domestica reveals innovation
in non-coding sequences.
Nature. 2007 May 10;447(7141):167-77.
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The Sumatran orangutan genome assembly (Pongo pygmaeus abelii) is
provided with the following acknowledgments:
- Sequencing:
- Sequence Assembly and Chromosomal Sequence/AGP Construction:
The Genome Institute at WUSTL
- DNA Source:
Dr. Greely Stones, Gladys Porter Zoo, Brownsville, TX, USA
- BAC Library:
Yuko Yoshonaga in Pieter de Jong's laboratory,
Children's Hospital Oakland Research Institute,
Oakland, CA, USA
- Fosmid Library: The Genome Institute at WUSTL
- Fingerprint Map: The Genome Institute at WUSTL
- Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses:
Mariano Rocchi, Department of Genetics and Microbiology,
University of Bari, Bari, Italy
- Fosmid End Placement against the Human Genome
(used for breakpoint/inversion analyses during AGP
construction): Lin Chen and Evan Eichler, Department of
Genome Sciences, University of Washington, Seattle, WA, USA
- Funding: National Human Genome Research
Institute (NHGRI), National Institutes of Health (NIH)
- UCSC Orangutan Genome Browser/Initial Annotations:
-
ponAbe2:
Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik
The orangutan genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP,
Wang Z, Chinwalla AT, Minx P et al.
Comparative and demographic analysis of orang-utan genomes.
Nature. 2011 Jan 27;469(7331):529-33.
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The panda (Ailuropoda melanoleuca) assembly was provided by
BGI-Shenzhen with the following acknowledgments:
The panda genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z
et al.
The sequence and de novo assembly of the giant panda genome.
Nature. 2010 Jan 21;463(7279):311-7.
PMID: 20010809
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The pig (Sus scrofa) assembly was provided with the following
acknowledgments:
-
Sequencing/Assembly:
-
UCSC Pig Genome Browser/Initial Annotations:
-
susScr3:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
-
susScr2:
Hiram Clawson, Brian Raney, Mark Diekhans, and Mary Goldman
The pig genome sequence has been released by the International Swine Genome
Sequencing Consortium under the terms of the
Toronto Statement.
The International Swine Genome Sequencing Consortium genome-wide analyses of
the pig genome is described in:
Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund LA, Schook LB.
Large-scale sequencing based on full-length-enriched cDNA
libraries in pigs: contribution to annotation of the pig genome draft
sequence. BMC Genomics. 2012 Nov 15;13:581.
PMID: 23150988
The initial marker paper:
Archibald AL, Bolund L, Churcher C, Fredholm M, Groenen MA, Harlizius B, Lee KT,
Milan D, Rogers J, Rothschild MF et al.
Pig genome sequence--analysis and publication strategy.
BMC Genomics. 2010 Jul 19;11:438.
PMID: 20642822;
PMCID: PMC3017778
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The pika genome assembly (Ochotona princeps) is provided with
the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Pika Genome Browser/Initial Annotations:
-
ochPri3:
Hiram Clawson, Brian Raney, and Steve Heitner
-
ochPri2:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The pika sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The pika data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The platypus genome assembly (Ornithorhynchus anatinus) is provided with the following acknowledgments:
The platypus genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F,
Belov K, Miller W, Clarke L, Chinwalla AT et al.
Genome analysis of the platypus reveals unique signatures of
evolution.
Nature. 2008 May 8;453(7192):175-83.
PMID: 18464734
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The proboscis monkey genome assembly (Nasalis larvatus) is provided
with the following acknowledgments:
- Sequencing/Assembly:
Proboscis Monkey Functional Genome Consortium
- UCSC Proboscis Monkey Genome Browser/Initial Annotations:
-
nasLar1:
Hiram Clawson and Jairo Navarro
The proboscis monkey sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The rabbit genome assembly (Oryctolagus cuniculus) is provided with
the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Rabbit Genome Browser/Initial Annotations:
-
oryCun2:
Hiram Clawson and Antonio Coelho
The rabbit genome data are made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The centers producing the data reserve the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The rat genome assembly (Rattus norvegicus) is provided by the
Rat Genome Sequencing Consortium with the following acknowledgments:
- Project Coordination:
Baylor College of Medicine Human Genome Sequencing
Center (BCM-HGSC)
- Funding:
- Sequencing:
- Assembly: BCM-HGSC ATLAS group - Rui Chen, James Durbin, Paul
Havlak
- Fingerprint Mapping:
The British Columbia Cancer
Agency Genome Sciences Center - Marco Marra, Jackie Schein
- BAC End Sequencing:
The Institute for Genomic Research - Shaying Zhao
- BAC Library Construction and Distribution:
Children's Hospital Oakland Research Institute (CHORI)
- Pieter deJong
- Rat Genome Database: Medical College of Wisconsin
- UCSC Rat Genome Browser/Initial Annotations:
-
rn6: Hiram
Clawson, Brian Raney and Matthew Speir
-
rn5: Hiram
Clawson, Brian Raney and Steve Heitner
-
rn4: Angie
Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil,
Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik
-
rn3: Hiram
Clawson, Heather Trumbower, Robert Kuhn, Yontao Lu, Terry Furey, Mark
Diekhans, Robert Baertsch, Donna Karolchik, and Jim Kent
The rat genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite these publications when using these data:
Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA.
The Atlas genome assembly system.
Genome Res. 2004 Apr;14(4):721-32.
PMID: 15060016
Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into
mammalian evolution.
Nature. 2004 Apr 1;428(6982):493-521.
PMID: 15057822
See the Baylor conditions of use web page for
restrictions on the use of these data.
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The UCSC Genome Browser displays multiple assemblies of the Rhesus macaque
genome produced by different institutions:
The BGI assembly is provided with the following acknowledgments:
-
Funding: Southern China Center for Innovative Pharmaceuticals (SCCIP),
the National Natural Science Foundation of China, the Shenzhen Municipal
Government of China, the Major State Basic Research Development Program of
China, the National Basic Research Program of China, and the National Science
and Technology Major Project of Key Drug Innovation and Development
-
Sequencing/Assembly: BGI, Shenzhen, China
The MMGSC assembly is provided with the following acknowledgments:
-
Funding:
National Human Genome Research Institute (NHGRI), USA
-
Sequencing/Assembly:
BCM-HGSC, Houston, TX, USA in collaboration with:
-
J. Craig Venter Science Foundation Joint Technology Center, Rockville, MD, USA
-
The Genome Institute at WUSTL, St. Louis, MO, USA
-
BAC resources:
Children's Hospital Oakland Research Institute (CHORI),
Oakland, CA, USA
-
BAC-based fingerprint map:
Genome Sciences Centre, Vancouver, B.C.
For more information on the MMGSC rhesus macaque genome project, see the BCM
HGSC
Rhesus Monkey Genome Project web page.
- UCSC Rhesus Genome Browser/Initial Annotations:
-
rheMac8:
Hiram Clawson, Christopher Lee, and Cath Tyner
-
rheMac3:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve
Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
-
rheMac2:
Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik
-
rheMac1 (archived): Robert Baertsch, Galt Barber, and Donna Karolchik
The initial sequencing and analysis of the rhesus macaque genome
produced by the MMGSC was published in: Rhesus Macaque Genome
Sequencing and Analysis Consortium.
Evolutionary and Biomedical Insights from the Rhesus Macaque
Genome. Science. 2007 Apr 13;316(5822):222-34.
PMID: 17431167
The initial sequencing and analysis of the rhesus macaque genome produced by
BGI was published in:
Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y,
van Gool AJ et al
Genome sequencing and comparison of two nonhuman primate animal
models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol.
2011 Oct 16;29(11):1019-23.
PMID: 22002653
The rhesus macaque sequence is made freely available for public use
with the following understanding:
- The data may be freely downloaded, used in analyses,
and repackaged in databases.
- Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider of
these data is properly acknowledged. For the rheMac1 and rheMac2 data, please
cite the BCM-HGSC web site or publications from BCM-HGSC referring to
the genome sequence.
- The BCM-HGSC and RMGSC plan to publish the assembly and
genomic annotation of the dataset, including large-scale
identification of regions of evolutionary conservation.
- This is in accordance with, and with the understandings
in the Fort Lauderdale meeting discussing
Community Resource Projects and the resulting
NHGRI policy statement.
- Any redistribution of the data should carry this notice.
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The rock hyrax genome assembly (Procavia capensis) is provided with
the following acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
-
UCSC Rock Hyrax Genome Browser/Initial Annotations:
-
proCap1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The rock hyrax sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The rock hyrax data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The sheep genome assembly (Ovis aries) is provided by the International
Sheep Genomics Consortium (ISGC) with the following acknowledgments:
The sheep genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite these publications when using these data:
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y,
Zhang W et al.
The sheep genome illuminates biology of the rumen and lipid
metabolism.
Science. 2014 Jun 6;344(6188):1168-73.
PMID: 24904168
International Sheep Genomics Consortium.
The sheep genome reference sequence: a work in progress.
Anim Genet. 2010 Oct;41(5):449-53.
PMID: 20809919
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The common shrew genome assembly (Sorex araneus) is provided with
the following acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Shrew Genome Browser/Initial Annotations:
-
sorAra2:
Hiram Clawson, Brian Raney, and Steve Heitner
-
sorAra1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The shrew sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The shrew data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The sloth genome assembly (Choloepus hoffmanni) is provided with
the following acknowledgments:
- Sequencing:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
- Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Sloth Genome Browser/Initial Annotations:
-
choHof1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The sloth sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The sloth data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The squirrel genome assembly (Spermophilus tridecemlineatus)) is
provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Squirrel Genome Browser/Initial Annotations:
-
speTri2:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The squirrel sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The squirrel data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The squirrel monkey genome assembly (Saimiri boliviensis) is provided
with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Squirrel Monkey Genome Browser/Initial Annotations:
-
saiBol1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The squirrel monkey genome sequence data are made available to the
public with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data set,
including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The tarsier genome assembly (Tarsius syrichta) is provided with
the following acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
-
UCSC Tarsier Genome Browser/Initial Annotations:
-
tarSyr2:
Hiram Clawson, Brian Raney, and Matthew Speir
-
tarSyr1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The tarsier sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The tarsier data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The Tasmanian devil genome assembly (Sarcophilus harrisii) is provided
with the following acknowledgments:
The Tasmanian devil genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B,
Hims M, Ding Z, Ivakhno S, Stewart C et al.
Genome sequencing and analysis of the Tasmanian devil and its
transmissible cancer.
Cell. 2012 Feb 17;148(4):780-91.
PMID: 22341448
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The tenrec genome assembly (Echinops telfairi) is provided by The
Broad Institute with the following acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Tenrec Genome Browser/Initial Annotations:
-
echTel2:
Hiram Clawson, Brian Raney and Steve Heitner
-
echTel1:
Hiram Clawson, Brian Raney and Steve Heitner
The tenrec genome sequence data are made available to the
public with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data set,
including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The tree shrew genome assembly (Tupaia belangeri) is provided with
the following acknowledgments:
- Funding: National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Tree Shrew Genome Browser/Initial Annotations:
-
tupBel1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The tree shrew sequence has been made freely available as
part of the Mammalian Genome Project (29 Mammals Project).
The initial analysis of this dataset can be found in
Lindblad-Toh K et al.
A high-resolution map of human evolutionary constraint using 29
mammals. Nature. 2011 Oct 12;478(7370):476-82.
PMID: 21993624;
PMCID: PMC3207357
The tree shrew data are provided with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
Any redistribution of the data should carry this notice.
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The wallaby genome assembly (Macropus eugenii) is provided with
the following acknowledgments:
The wallaby genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W,
Waters PD, Pharo EA, Shaw G et al.
Genome sequence of an Australian kangaroo, Macropus eugenii,
provides insight into the evolution of mammalian reproduction and
development.
Genome Biol. 2011 Aug 29;12(8):R81.
PMID: 21854559
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The southern white rhinoceros genome assembly (Ceratotherium simum) is
provided with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
- Data Samples:
Dr. Oliver Ryder, San Diego Zoo Institute for
Conservation Research, San Diego, CA
-
UCSC White Rhinoceros Genome Browser/Initial Annotations:
-
cerSim1:
Hiram Clawson and Steve Heitner
The southern white rhinoceros sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The centers producing the data reserve the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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American Alligator Genome
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The American alligator assembly (Alligator mississippiensis) is
provided by the International Crocodilian Genomes Working Group with the
following acknowledgments:
The American alligator genome data may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite this publication when using these data:
St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P,
Moran C, Bed'hom B, Abzhanov A et al.
Sequencing three crocodilian genomes to illuminate the evolution
of archosaurs and amniotes.
Genome Biol. 2012 Jan 31;13(1):415.
PMID: 22293439
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The Atlantic cod genome assembly (Gadus morhua) is provided with the
following acknowledgments:
- Funding:
Research Council of Norway (FUGE)
- Sequencing/Assembly:
GenoFisk Consortium
-
UCSC Atlantic Cod Genome Browser/Initial Annotations:
-
gadMor1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The Atlantic cod genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite these publications when using these data:
Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T,
Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T et al.
Large-scale sequence analyses of Atlantic cod.
N Biotechnol. 2009 Jun;25(5):263-71.
PMID: 19491044
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF,
Rounge TB, Paulsen J, Solbakken MH, Sharma A et al.
The genome sequence of Atlantic cod reveals a unique immune
system.
Nature. 2011 Aug 10;477(7363):207-10.
PMID: 21832995
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The budgerigar genome assembly (Melopsittacus undulatus) is provided
with the following acknowledgments:
- Sequencing/Assembly:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
-
UCSC Budgerigar Genome Browser/Initial Annotations:
-
melUnd1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The budgerigar sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The centers producing the data reserve the right to
publish the initial large-scale analyses of the data set,
including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome.
-
This is in accordance with, and with the understandings
in the Fort Lauderdale meeting
discussing Community Resource Projects and the resulting
NHGRI policy statement.
-
Any redistribution of the data should carry this notice.
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The chicken genome assembly (Gallus gallus) is provided with
the following acknowledgments:
- Sequencing:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
- Physical Map: The Genome Institute at WUSTL
- Genetic Mapping/Linkage Analysis: The Chicken Mapping Consortium:
-
Wageningen Map based on Wageningen broilerxbroiler mapping population
("W" linkage maps; 460 F2 animals), coordinated by Martien Groenen,
Wageningen University, Wageningen, The Netherlands
-
East Lansing Map based on the RJFxlayer cross ("E" linkage maps; 56 BC
animals), coordinated by Hans Cheng,
USDA-ARS, East Lansing, MI, USA
-
Compton map based on layerxlayer cross ("C" linkage maps; 52 BC animals),
coordinated by Nat Bumstead, Institute for Animal Health
-
Consensus linkage map: Martien Groenen and Richard Crooijmans, Wageningen
University
-
RH map: coordinated by Mireille Morisson and Alain Vignal,
French National Institute for Agricultural Research
(INRA), Toulouse
-
Linkage Mapping: White Leghorn X Red Junglefowl (800 F2 animals),
coordinated by Susanne Kerje, Lina Jacobsson and Leif Andersson,
Uppsala University, Uppsala, Sweden
-
Clone/Marker Pairs: coordinated by Jerry Dodgson,
Michigan State University, East Lansing, MI, USA
-
Marker Name/Sequence Resolution: coordinated by Hans
Cheng, USDA-ARS, East Lansing, MI, USA
-
Chicken FPC browser:
ChickFPC, Martien Groenen and Richard
Crooijmans (galGal3), Jan Aerts (galGal2),
Wageningen University
-
Additional Mapping Data Contributions: Winston Bellott,
David Page Lab,
Whitehead Institute for Biomedical Research (WIBR-MIT),
Cambridge, MA, USA
-
cDNA sequences: National Institutes of Health and The University of
Manchester BBSRC ChickEST Database
-
RJF finished clones:
-
Assembly, Assembly/Map Integration, Golden Path
Creation: The Genome Institute at WUSTL
-
SNPs and cross-referenced gene annotations:
The Beijing Genomics Institute (BGI),
Beijing, China
-
UCSC Chicken Genome Browser/Initial Annotations:
-
galGal5:
Hiram Clawson, Brian Raney and Matthew Speir
-
galGal4:
Hiram Clawson, Brian Raney and Steve Heitner
-
galGal3:
Angie Hinrichs, Kayla Smith, Donna Karolchik
-
galGal2:
Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik
The chicken genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide
unique perspectives on vertebrate evolution.
Nature. 2004 Dec 9;432(7018):695-716.
PMID: 15592404
The BGI gene annotations and SNP data are made available with the following
terms of use:
-
Users are free to use these data in scientific papers analyzing particular
genes, if the Beijing Genomics Institute (BGI) is acknowledged.
-
BGI and its collaborators reserve the right to publish the
initial analyses of these data, including but not restricted
to the large-scale identification of functional polymorphisms,
evolutionary patterns and signs of selection, correlations
with known QTLs, utility of data for genetic mapping
purposes, etc.
-
Any redistribution of these data should carry this notice.
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The coelacanth genome assembly (Latimeria chalumnae) is provided with
the following acknowledgments:
- Funding:
National Human Genome Research Institute (NHGRI)
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Coelacanth Genome Browser/Initial Annotations:
-
latCha1:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The coelacanth genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch
I, Manousaki T, Schneider I, Rohner N et al.
The African coelacanth genome provides insights into tetrapod
evolution.
Nature. 2013 Apr 18;496(7445):311-6.
PMID: 23598338
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The elephant shark genome assembly (Callorhinchus milii) is provided
by the Singapore Institute of Molecular and Cell Biology with the following
acknowledgments:
The elephant shark genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF,
Sutoh Y, Kasahara M et al.
Elephant shark genome provides unique insights into gnathostome
evolution.
Nature. 2014 Jan 9;505(7482):174-9.
PMID: 24402279
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The Fugu genome assembly (Takifugu rubripes) is provided by the
Joint Genome Institute (JGI) as
part of the International Fugu Genome Consortium, led by the JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
The assembly has the following acknowledgments:
-
Sequencing/Assembly:
Assembly was constructed with the JGI assembler, JAZZ, from paired end
sequencing reads produced by JGI and the IMCB at JGI, Myriad Genetics, and
Celera Genomics
-
UCSC Fugu Genome Browser/Initial Annotations:
-
fr3:
Hiram Clawson and Greg Roe
-
fr2:
Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik
-
fr1:
Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik
The Fugu genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H,
Naruse K, Brenner S et al.
Integration of the genetic map and genome assembly of fugu
facilitates insights into distinct features of genome evolution in teleosts and
mammals.
Genome Biol Evol. 2011;3:424-42.
PMID: 21551351
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The lamprey genome assembly (Petromyzon marinus) is provided with
the following acknowledgments:
The lamprey genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD,
Manousaki T, Meyer A et al.
Sequencing of the sea lamprey (Petromyzon marinus) genome
provides insights into vertebrate evolution.
Nat Genet. 2013 Apr;45(4):415-21, 421e1-2.
PMID: 234350859
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The lizard genome assembly (Anolis carolinensis) is provided by The
Broad Institute with the following acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA USA
-
UCSC Lizard Genome Browser/Initial Annotations:
-
anoCar2:
Hiram Clawson, Brian Raney, Luvina Guruvadoo, and Donna Karolchik
-
anoCar1:
Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik
The lizard genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E,
Russell P, Lowe CB, Glor RE, Jaffe JD et al.
The genome of the green anole lizard and a comparative analysis
with birds and mammals.
Nature. 2011 Aug 31;477(7366):587-91.
PMID: 21881562
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The medaka genome assembly (Oryzias latipes) is provided by
Japan's National Institute of Genetics
(NIG) and the University of Tokyo.
The assembly was constructed using the RAMEN assembler.
NOTE: The UCSC oryLat1 assembly was replaced by
oryLat2 in
Nov. 2008 to correct a UCSC assembly error with chrUn in
which the gap relationships between contigs within their
ultracontigs were broken. The oryLat2 assembly is based on the same assembly as oryLat1:
the v1.0 assembly from NIG and the University of Tokyo.
-
Sequencing/Assembly: NIG and University of Tokyo, Japan
-
UCSC Medaka Genome Browser/Initial Annotations:
-
oryLat2:
Hiram Clawson, Pauline Fujita, and Donna Karolchik
The medaka genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y,
Doi K, Kasai Y et al.
The medaka draft genome and insights into vertebrate genome
evolution.
Nature. 2007 Jun 7;447(7145):714-9.
PMID: 17554307
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Medium Ground Finch Genome
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The medium ground finch genome assembly (Geospiza fortis) is the
product of a collaboration between the Genome 10K Project and
Beijing Genomics Institute (BGI). The data are provided
with the following acknowledgments:
-
Sequencing/Assembly: Genome 10K Project and Beijing Genomics
Institute (BGI)
-
UCSC Medium Ground Finch Genome Browser/Initial Annotations:
-
geoFor1:
Hiram Clawson and Greg Roe
The medium ground finch genome data may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite this publication when using these data:
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C5, Storz JF, Antunes A, Greenwold MJ,
Meredith RW et al.
Comparative genomics reveals insights into avian genome
evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20.
PMID: 25504712;
PMCID: PMC4390078
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The Nile tilapia genome assembly (Oreochromis niloticus) is provided
with the following acknowledgments:
- Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Nile Tilapia Genome Browser/Initial Annotations:
-
oreNil2:
Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
The Nile tilapia genome data may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite this publication when using these data:
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY,
Lim ZW, Bezault E et al.
The genomic substrate for adaptive radiation in African cichlid
fish. Nature. 2014 Sep 18;513(7518):375-81.
PMID: 25186727;
PMCID: PMC4353498
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The painted turtle genome assembly (Chrysemys picta bellii) is provided
with the following acknowledgments:
-
Sequencing/Assembly: International Painted Turtle Genome Sequencing
Consortium
-
UCSC Painted Turtle Genome Browser/Initial Annotations:
-
chrPic1:
Hiram Clawson, Brian Raney and Steve Heitner
The painted turtle genome data may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite this publication when using these data:
Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y,
Minx P, Janes DE, Warren WC, Edwards SV et al.
Physical mapping and refinement of the painted turtle genome
(Chrysemys picta) inform amniote genome evolution and challenge turtle-bird
chromosomal conservation.
Genome Biol Evol. 2015 Jun 24;7(7):2038-50.
PMID: 26108489;
PMCID: PMC4524486
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The stickleback genome assembly (Gasterosteus aculeatus) is provided
by The Broad Institute with the following acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA USA
-
UCSC Stickleback Genome Browser/Initial Annotations:
-
gasAcu1:
Angie Hinrichs, Hiram Clawson, Kayla Smith, and Donna Karolchik
The stickleback sequence is made freely available before
scientific publication with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The Tetraodon genome assembly (Tetraodon nigroviridis) is provided with
the following acknowledgments:
-
Sequencing/Assembly:
-
Project Funding:
-
Initial Genome Browser Annotations:
-
Genoscope - Genscan gene predictions, GAZE gene predictions
-
UCSC Genome Bioinformatics Group, University of
California, Santa Cruz, CA, USA - remaining annotations (based on data from
Genoscope)
-
UCSC Tetraodon Genome Browser:
-
tetNig2:
Hiram Clawson, Mark Diekhans, Brian Raney, Ann Zweig, Mary Goldman, Vanessa
Swing, Antonio Coelho, Robert Kuhn, and Donna Karolchik
-
tetNig1:
Rachel Harte, Robert Kuhn, Donna Karolchik
The Tetraodon genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Yue GH, Lo LC, Zhu ZY, Lin G, Feng F.
The complete nucleotide sequence of the mitochondrial genome of
Tetraodon nigroviridis. DNA Seq. 2006 Apr;17(2):115-21.
PMID: 17076253
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The Tibetan Frog genome assembly (Nanorana parkeri) is provided
by BGI-Shenzhen with the following acknowledgments:
The Tibetan frog genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, Zhong L, Wang L, Wu DD,
Zhang BL et al.
Whole-genome sequence of the Tibetan frog Nanorana parkeri and
the comparative evolution of tetrapod genomes.
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1257-62.
PMID: 25733869;
PMCID: PMC4371989
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The turkey genome assembly (Meleagris gallopavo) is provided with
the following acknowledgments:
The turkey genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann,
Bouffard P, Burt DW, Crasta O, Crooijmans RP et al.
Multi-platform next-generation sequencing of the domestic turkey
(Meleagris gallopavo): genome assembly and analysis.
PLoS Biol. 2010 Sep 7;8(9).
PMID: 20838655
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The Xenopus (Silurana) tropicalis genome assembly is provided by the
Joint Genome Institute (JGI)
with the following acknowledgments:
-
Sequencing/Assembly: JGI, Walnut Creek, CA, USA
-
UCSC X. tropicalis Genome Browser/Initial Annotations:
-
xenTro7:
Hiram Clawson, Brian Raney, and Matthew Speir
-
xenTro3:
Hiram Clawson, Brian Raney, Brooke Rhead, Greg Roe, Steve
Heitner, and Donna Karolchik
-
xenTro2:
Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik
-
xenTro1:
Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney,
Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik
The X. tropicalis genome data may be freely downloaded, used in
analyses, and repackaged in databases if the data provider is properly
acknowledged. Please cite this publication when using these data:
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V,
Ovcharenko I, Putnam NH, Shu S, Taher L et al.
The genome of the Western clawed frog Xenopus tropicalis.
Science. 2010 Apr 30;328(5978):633-6.
PMID: 20431018
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The zebra finch genome assembly (Taeniopygia guttata) is
provided by the Genome Institute at Washington University (WUSTL)
with the following acknowledgments:
-
Sequencing/Assembly:
The Genome Institute at WUSTL, St. Louis, MO, USA
-
Zebra finch DNA:
Arthur P. Arnold lab, Dept. of Physiological Science,
UCLA, Los Angeles, CA, USA
-
UCSC Zebra Finch Genome Browser/Initial Annotation:
-
taeGut2:
Hiram Clawson, Brian Raney, and Steve Heitner
-
taeGut1:
Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik
The zebra finch genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A,
Searle S, White S, Vilella AJ, Fairley S et al.
The genome of a songbird.
Nature. 2010 Apr 1;464(7289):757-62.
PMID: 20360741
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Starting with the danRer10 (GRCz10) assembly, the zebrafish genome sequence is
now provided by the
Genome Reference Consortium (GRC).
Prior assemblies have the following acknowledgments:
-
Sequencing/Assembly:
The Wellcome Trust Sanger Institute, UK.
-
FPC map:
-
BAC Clones, BAC End Pairs:
-
The Wellcome Trust Sanger Institute, UK - GenBank
accessions for BAC clones
-
Max-Planck Institute for Developmental
Biology, Germany - BAC end pairs sequence data
-
Hubrecht Laboratory, Netherlands Institute
for Developmental Biology, The Netherlands - BAC end pairs
sequence data
-
Annotations:
-
Yi Zhou, Anthony DiBiase, Leonard Zon and the Zebrafish
Genome Initiative at Boston Children's Hospital, Boston, MA, US -
collaboration on Zebrafish WZ EST clusters, BAC End Singles/Pairs, Radiation
Hybrid, and Human tBLASTn annotation tracks
-
Washington University in St. Louis, St.
Louis, MO, US - Zebrafish WZ EST clusters data
-
Ensembl,
UK - Ensembl gene predictions
-
UCSC Genome Bioinformatics Group, University of
California, Santa Cruz, CA, USA - Other annotations
-
UCSC Zebrafish Genome Browsers:
-
danRer10: Hiram Clawson, Brian Raney, Steve Heitner
-
danRer7: Hiram Clawson, Mary Goldman, Greg Roe, Brian
Raney, Donna Karolchik
-
danRer6: Galt Barber, Robert Kuhn, Katrina Learned,
Donna Karolchik
-
danRer5: Rachel Harte, Ann Zweig, Donna Karolchik
-
danRer4: Rachel Harte, Archana Thakkapallayil, Robert
Kuhn, Ann Zweig, Donna Karolchik
-
danRer3: Rachel Harte, Jennifer Jackson, Ann Zweig,
Ali Sultan-Qurraie, Donna Karolchik
-
danRer2 (archived): Rachel Harte,
Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson
The zebrafish genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE,
Humphray S, McLaren K, Matthews L et al.
The zebrafish reference genome sequence and its relationship
to the human genome.
Nature. 2013 Apr 25;496(7446):498-503.
PMID: 23594743
For more information about zebrafish assemblies provided by the GRC, see the
GRC zebrafish web pages. For information about assemblies
prior to danRer10/GRCz10, see the Sanger Institute's
Zebrafish Sequencing Project web page.
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The C. intestinalis v1.0 and v2.0 draft assemblies are provided
by the Joint Genome Institute (JGI) with the
following acknowledgments:
-
Project Funding: Work performed under the auspices of
the US Department of Energy's Office of Science, Biological
and Environmental Research Program and the by the University
of California, Lawrence Livermore National Laboratory under
Contract No. W-7405-Eng-48, Lawrence Berkeley National
Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos
National Laboratory under contract No. W-7405-ENG-36.
-
Project Collaborators:
-
JGI, Walnut Creek, CA, USA
-
Department of Zoology, Graduate School of Science, Kyoto
University, Kyoto, Japan
-
Department of Molecular
and Cellular Biology, University of California, Berkeley, CA, USA
-
National Institute of Genetics, Mishima,
Japan
-
Oak Ridge National
Laboratory, Oak Ridge, TN, USA
-
Los Alamos National
Laboratory, Los Alamos, NM, USA
-
Annotations:
-
Colin Dewey, University of California, Berkeley, CA, USA -
SNAP Gene Predictions, using the SNAP parser written by Ian Korf
-
JGI, Walnut Creek, CA, USA - JGI Gene Predictions
-
UCSC Genome Bioinformatics Group, University
of California, Santa Cruz, CA, USA - Other annotations
-
UCSC C. intestinalis Genome Browsers:
-
ci2: Brian
Raney, Mark Diekhans, Ann Zweig, Kayla Smith, Robert Kuhn, Donna Karolchik
-
ci1: Brian
Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik
The C. intestinalis sequence data have been freely provided by the
JGI and may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B,
Di Gregorio A, Gelpke M, Goodstein DM et al.
The draft genome of Ciona intestinalis: insights into chordate
and vertebrate origins. Science. 2002 Dec 13;298(5601):2157-67.
PMID: 12481130
For more information about the C. intestinalis assembly, see the JGI
C. intestinalis portal.
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The lancelet (Branchiostoma floridae) genome assembly is provided
by the Joint Genome Institute (JGI) with the following acknowledgments:
-
Funding:
U.S. Department of Energy Office of Science, Biological
and Environmental Research Program
-
Sequencing/Assembly:
JGI
-
UCSC Lancelet Genome Browser/Initial Annotations:
-
braFlo1:
Hiram Clawson, Ann Zweig, Pauline Fujita, Donna Karolchik
The lancelet genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T,
Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK et al.
The amphioxus genome and the evolution of the chordate
karyotype.
Nature. 2008 Jun 19;453(7198):1064-71.
PMID: 18563158
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The sea urchin (Strongylocentrotus purpuratus) genome assembly
is provided by the Baylor College of Medicine Human Genome Sequencing Center
(BCM-HGSC). The assemblies available in the browser include:
-
Sep. 2006 strPur2 browser: Baylor version Spur 2.1 (NCBI v2.1)
-
Apr. 2005 strPur1 browser: Baylor version Spur_0.5 (NCBI v1.1)
These data are provided with the following acknowledgments:
The sea urchin genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite this publication when using these data:
Sea Urchin Genome Sequencing Consortium.
The genome of the sea urchin Strongylocentrotus purpuratus.
Science. 2006 Nov 10;314(5801):941-52.
PMID: 17095691
For more information on the sea urchin genome project, see the BCM-HGSC
Sea Urchin Genome Project web page.
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The MOZ2 Anopheles gambiae data were provided by the
International Anopheles Genome Project and downloaded from Ensembl. The data
have the following acknowledgments:
-
Funding:
National Institute of Allergy and Infectious Diseases
(NIAID), French Ministry of Research, and the
World Health Organization
(WHO). Celera Genomics and Genoscope
were funded respectively by National Institutes of Health (NIH) and the
French Ministry of Research.
-
Project collaboration:
The International Anopheles Genome Project - a collaboration between
Celera Genomics,
Genoscope,
University of Notre Dame,
EBI/Sanger Institute,
EMBL,
Institut Pasteur,
The Institute of Molecular Biology and Biotechnology
(IMBB) and The Institute for Genomic Research (TIGR).
-
Sequencing and Assembly:
Celera Genomics,
Genoscope
-
Data Downloads:
Ensembl
-
UCSC A. gambaie Genome Browser/Initial Annotations:
- anoGam1:
Angie Hinrichs, Galt Barber, Donna Karolchik
-
Additional Genome Browser Annotations:
Ensembl and
Celera Genomics
(Ensembl Genes)
The A. gambaie sequence is made freely available
by the International Anopheles Genome Project. Please cite the following
publication when using these data:
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker
P, Clark AG, Ribeiro JM, Wides R et al.
The genome sequence of the malaria mosquito Anopheles gambiae.
Science. 2002 Oct 4;298(5591):129-49.
PMID: 12364791
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The Amel_1.2 data were provided by the
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)
with the following acknowledgments:
-
Funding:
National Human
Genome Research Institute (NHGRI) and the
U.S. Department of Agriculture (USDA)
-
Sequencing and assembly:
BCM-HGSC, Houston, TX, USA
-
BAC library:
Pieter de Jong and Katzutoyo Osoegawa at
Children's Hospital Oakland Research
Institute (CHORI), Oakland, CA, USA
-
UCSC A. mellifera Genome Browser/Initial Annotations:
- apiMel2:
Andy Pohl, Angie Hinrichs, Jennifer Jackson, Donna Karolchik
- apiMel1:
Angie Hinrichs, Brian Raney, Robert Kuhn, Donna Karolchik
The A. mellifera sequence is made freely available
by the Honeybee Genome Sequencing Consortium. Please cite the following
publication when using these data:
Honeybee Genome Sequencing Consortium.
Insights into social insects from the genome of the honeybee
Apis mellifera.
Nature. 2006 Oct 26;443(7114):931-49.
PMID: 17073008
See the Baylor conditions of use statement for guidelines regarding the
use of these data.
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The droAna2 data were provided by Agencourt
Bioscience. The droAna1 data were produced by the Institute
for Genomic Research (TIGR). The D. ananassae
Genome Browser has the following acknowledgments:
-
Sequencing:
Agencourt Bioscience,
Danvers, MA, USA
-
Assembly:
-
UCSC D. ananassae Genome Browser (droAna2):
Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith, and
Donna Karolchik
-
UCSC D. ananassae Genome Browser (droAna1):
Angie Hinrichs, Brian Raney, Heather Trumbower, Ali
Sultan-Qurraie, and Donna Karolchik
-
Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. ananassae sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite these publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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The droEre1 data were provided by
Agencourt Bioscience. The
D. erecta Genome Browser has the following
acknowledgments:
-
Sequencing and Assembly:
Agencourt Bioscience,
Danvers, MA, USA, using the
Arachne assembler
-
UCSC D. erecta Genome Browser (droEre1):
Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna
Karolchik
-
Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. erecta sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite these publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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The droGri data were provided by
Agencourt Bioscience. The
D. grimshawi Genome Browser has the following
acknowledgments:
-
Sequencing and Assembly:
Agencourt Bioscience,
Danvers, MA, USA, using the
Arachne assembler
-
UCSC D. grimshawi Genome Browser (droGri1):
Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith
and Donna Karolchik
-
Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. grimshawi sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite these publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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The D. melanogaster assemblies displayed in the
UCSC Genome Browser were obtained from the
Berkeley
Drosophila Genome Project (BDGP) with the following
acknowledgments:
- Sequencing and Assembly:
- Annotations:
- Euchromatic regions -
FlyBase
- Heterochromatic regions -
DHGP, Lawrence Berkeley
National Laboratory, Berkeley, CA, USA
- UCSC D. melanogaster Genome Browser
and additional annotations (dm6):
Hiram Clawson, Angie Hinrichs, and Matthew Speir
- UCSC D. melanogaster Genome Browser
and additional annotations (dm3):
Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and
Donna Karolchik -
UCSC Genome
Bioinformatics Group, UCSC, Santa Cruz, CA, USA
- UCSC D. melanogaster Genome Browser
and additional annotations (dm2):
Angie Hinrichs, Brian Raney, Galt Barber,
and Donna Karolchik -
UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
- UCSC D. melanogaster Genome Browser
and additional annotations (dm1):
Angie Hinrichs, Brian Raney, Heather Trumbower, Ali
Sultan-Qurraie, and Donna Karolchik -
UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
For additional information about these data, including
citation guidelines, see the
BDGP web site.
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These data were produced by Agencourt
Bioscience. The D. mojavensis Genome Browser
has the following acknowledgments:
-
Sequencing and Assembly:
Agencourt Bioscience,
Danvers, MA, USA, using the
Arachne assembler
-
Funding:
National Human
Genome Research Institute (NHGRI), USA
-
UCSC D. mojavensis Genome Browser (droMoj2):
Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna
Karolchik
-
UCSC D. mojavensis Genome Browser (droMoj1):
Angie Hinrichs, Brian Raney, Galt Barber and Donna
Karolchik
-
Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. mojavensis sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite these publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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The droPer1 assembly was provided with the following acknowledgments:
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Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC D. persimilis Genome Browser (droPer1):
Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson
and Donna Karolchik
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Initial Genome Browser Annotations:
UCSC Genome Bioinformatics Group,
University of California,
Santa Cruz, CA, USA
The D. persimilis sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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These data were produced by the
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC).
The D. pseudoobscura Genome Browser has the following
acknowledgments:
-
Sequencing and Assembly:
BCM-HGSC, Houston, TX, USA
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UCSC D. pseudoobscura Genome Browser (dp3):
Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna
Karolchik
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UCSC D. pseudoobscura Genome Browser (dp2):
Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna
Karolchik
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Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. pseudoobscura data are made available with
specific conditions for use. Please cite the following
publications:
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R,
Thornton K, Hubisz MJ, Chen R, Meisel RP et al.
Comparative genome sequencing of Drosophila pseudoobscura:
chromosomal, gene, and cis-element evolution.
Genome Res. 2005 Jan;15(1):1-18.
PMID: 15632085;
PMCID: PMC540289
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
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The droSec1 assembly was provided with the following acknowledgments:
The D. sechellia sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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These data were provided with the following acknowledgments:
-
Sequencing and assembly:
The Genome Institute at Washington University (WUSTL),
St. Louis, MO, USA
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UCSC D. simulans Genome Browser
(droSim1):
Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie,
Brian Raney and Donna Karolchik
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Initial Genome Browser Annotations:
UCSC Genome Bioinformatics Group,
University of California, Santa Cruz, CA, USA
The D. simulans sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
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These data were produced by Agencourt
Bioscience. The D. virilis Genome Browser
has the following acknowledgments:
-
Sequencing and Assembly:
Agencourt Bioscience,
Danvers, MA, USA, using the
Arachne assembler
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Funding:
National Human
Genome Research Institute (NHGRI), USA
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UCSC D. virilis Genome Browser (droVir2):
Angie Hinrichs, Brian Raney, Jennifer Jackson and
Donna Karolchik
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UCSC D. virilis Genome Browser (droVir1):
Angie Hinrichs, Brian Raney, Heather Trumbower,
Robert Kuhn, Jennifer Jackson, and Donna Karolchik
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Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. virilis sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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These data were provided by The Genome Institute at
Washington University (WUSTL) with the following acknowledgments:
-
Funding:
National Human
Genome Research Institute (NHGRI)
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Sequencing, assembly and AGP creation:
The Genome Institute at Washington University (WUSTL)
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Initial Sequencing Proposal, Project Collaboration:
David J. Begun and Charles H. Langley,
University of California, Davis, CA, USA
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UCSC D. yakuba Genome Browser (droYak2):
Angie Hinrichs, Jennifer Jackson and Donna Karolchik
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UCSC D. yakuba Genome Browser (droYak1):
Angie Hinrichs, Michael Chalup and Donna Karolchik
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Initial Genome Browser Annotations:
UCSC Genome
Bioinformatics Group, University of California,
Santa Cruz, CA, USA
The D. yakuba sequence may be freely downloaded, used in analyses,
and repackaged in databases if the data provider is properly acknowledged.
Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium.
Evolution of genes and genomes on the Drosophila phylogeny.
Nature. 2007 Nov 8;450(7167):203-18.
PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA.
Assembly reconciliation. Bioinformatics.
2008 Jan 1;24(1):42-5.
PMID: 18057021
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Worm Genomes (other than C. elegans)
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The latest versions of the C. brenneri,
C. briggsae, C. japonica,
C. remanei, and P. pacificus sequences
were obtained from the Genome Sequencing Center at
The Genome Institute at Washington University (WUSTL).
The cb1 browser data
were obtained from WormBase.
We'd like to thank WUSTL for providing the sequence data
for these assemblies, as well as the Sanger Institute for
their collaborative work in sequencing the initial
C. briggsae cb1 genome. Thanks also to the
WormBase consortium for providing access to the cb1
sequence.
The worm sequences are made freely available with the following understanding:
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The data may be freely downloaded, used in analyses, and
repackaged in databases.
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Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The centers producing the data reserve the right to
publish the initial large-scale analyses of the data set,
including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome.
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This is in accordance with, and with the understandings
in the Fort Lauderdale meeting
discussing Community Resource Projects and the resulting
NHGRI policy statement.
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Any redistribution of the data should carry this notice.
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UCSC Sacchromyces cerevisiae Genome Browser (sacCer3): Hiram Clawson,
Greg Roe, Steve Heitner.
The April 2011 Sacchromyces cerevisiae genome assembly
is based on sequence dated April 2011 in the
Sacchromyces Genome
Database (SGD). This genome sequence was downloaded from
NCBI (genbank/genomes/Eukaryotes/fungi/Saccharomy
ces_cerevisiae/SacCer_Apr2011/). The SGD™ gene annotations were downloaded
from the SGD downloads site. The S288C strain was used in this sequencing project.
The June 2008 Sacchromyces cerevisiae genome assembly
(sacCer2)
is based on sequence dated June 2008 in the
Sacchromyces Genome
Database (SGD) and was obtained from the site
http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/
The S288C strain was used in this sequencing project.
The Oct. 2003 Sacchromyces cerevisiae genome assembly
(sacCer1)
is based on sequence dated 1 Oct. 2003 in the
Sacchromyces Genome
Database (SGD). The sequence, open reading frame (ORF),
and gene annotations were downloaded from the site
http://www.yeastgenome.org/download-data/sequence.
The cellular localization and protein abundance data displayed
in the Gene Sorter are taken from the
Yeast GFP
Fusion Localization Database.
See the SGD
Systematic Sequencing Table for credit and
contact information for each of the chromosomes in the
assembly. We'd like to thank Stanford University, the SGD,
the University of California San Francisco (UCSF),
Washington University in St. Louis, and The Broad
Institute
for providing the data and annotations for this release.
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California Sea Hare Genome
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The Aplysia californica genome assembly
has the following acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
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UCSC California Sea Hare (aplCal1) Genome Browser:
Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned and Donna Karolchik
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Initial Genome Browser Annotations:
UCSC Genome Bioinformatics Group,
University of California, Santa Cruz, CA, USA
The California sea hare sequence is made freely available
with the following understanding:
-
The data may be freely downloaded, used in analyses, and
repackaged in databases.
-
Users are free to use the data in scientific papers
analyzing particular genes and regions if the provider
of these data is properly acknowledged.
-
The center producing the data reserves the right to
publish the initial large-scale analyses of the data
set, including large-scale identification of regions of
evolutionary conservation and large-scale genomic
assembly. Large-scale refers to regions with size on the
order of a chromosome (that is, 30 Mb or more).
-
Any redistribution of the data should carry this notice.
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The Ebola virus genome assembly
has the following acknowledgments:
-
Sequencing/Assembly:
The Broad Institute, Cambridge, MA, USA
-
UCSC Ebola virus (eboVir3) Genome Browser:
Hiram Clawson, Brian Raney, Maximillian Haeussler, Angie Hirichs, Kate
Rosenbloom, Chris Eisenhart, Pauline Fujita, Matthew Speir, Donna
Karolchik, Ann Zweig, David Haussler, and Jim Kent
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Initial Genome Browser Annotations:
UCSC Genome Bioinformatics Group,
University of California, Santa Cruz, CA, USA
Other Acknowledgements:
Thank you to
Phillip Berman and his lab at UCSC for providing continued
feedback on the Ebola virus Genome Browser, and to the
Pardis Sabeti Lab at
the Broad Institute for their guidance.
Thank you to the following institutions for proving additional annotations
on the Ebola virus genome:
The Ebola virus sequence may be freely downloaded, used in analyses,
and repackaged in databases. The data may be freely used in scientific
papers analyzing particular genes and regions if the provider of these
data is properly acknowledged.
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Acknowledgment of Early Support
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During the initial stage of this project, from January 2000 to June 2001,
we received no direct federal funding to develop the working draft other than
travel support. However, we gratefully acknowledge the support for our
personnel provided by our basic bioinformatics research grants, especially
DOE grant DE-FG03-99ER62849 (to develop gene-finding methods), but also NSF
grant DBI-9809007, UC BIOTECH grant 99-11, a grant from the Sloan Foundation,
the David and Lucille Packard Foundation, NIH grant GM-52848, and the Zahler
grant that provided support for Jim Kent in the early stages of this work.
We are particularly thankful for the risks that Patrick Mantey (UCSC Dean of
Engineering), James Gill (Vice Chancellor for Research), John Simpson (UCSC
Provost), and M.R.C. Greenwood (UCSC Chancellor) were willing to take
in advancing us the money in February 2000 needed to build the original
100-node LINUX cluster used in this work, and in the case of Dean Mantey,
additional personnel support. Phokion Kolaitis, Chair of Computer Science,
contributed as well.
We thank Compaq for
providing an additional 100-CPU computational cluster in Cambridge, MA for use
by the public human genome effort. We thank ILOG, Inc. (now part of IBM) for providing discounted licenses to its CPLEX
linear programming software, which was essential for some of our early
experiments.
In December 2000, HHMI
began providing support for equipment and personnel. In the summer of 2001,
HHMI provided the primary funding for a new cluster of 1000 CPUs running
LINUX purchased from
Rackable (now SGI), with additional support from
CISI
and NHGRI. Dubbed the
UCSC KiloKluster, this equipment became the computational backbone
for the initial years of the Genome Browser project.
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