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  UCSC Genome Browser Acknowledgments

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

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  Human Genome Browser: Acknowledgments
HHMI CISI
NHGRI

The UCSC Human Genome Browser is generated by the UCSC Genome Bioinformatics Groupin 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 project team acknowledgments:

  • UCSC Human Genome Browser (hg38): Hiram Clawson, Brian Raney, Robert Kuhn, Donna Karolchik, Steve Heitner
  • UCSC Human Genome Browser (hg19): Hiram Clawson, Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned, Donna Karolchik and Robert Kuhn
  • UCSC Human Genome Browser (hg18): Engineering effort led by Fan Hsu; QA effort led by Ann Zweig
  • UCSC Human Genome Browser (hg17): Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik, Kate Rosenbloom, Angie Hinrichs, Rachel Harte, and Jim Kent
  • UCSC Human Genome Browser (hg16): Terry Furey, Hiram Clawson, Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent
  • UCSC Human Genome Browser (hg15): 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 the many other students in the UCSC Genome Bioinformatics group
  • Early Human Genome Browsers: UCSC Genome Bioinformatics staff and students

  Human Genome: Data Sources

Starting with the hg19 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 in 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 people 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 		Jane Rogers
2 The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA 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 		Steve Scherer
4 The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Rick Wilson
5 Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Jeremy Schmutz
6 The Wellcome Trust Sanger Institute, Cambridge, UK Jane Rogers
7 The Genome Institute at Washington University (WUSTL), St. Louis, MO USA
University of Washington, Department of Genome Sciences, Seattle, WA, USA 		Rick Wilson
8 The Broad Institute, Cambridge, MA USA
Keio University, Tokyo, Japan
Institute of Molecular Biology (IMB), Jena, Germany 		Chad Nusbaum
9 The Wellcome Trust Sanger Institute, Cambridge, UK
Gesellschaft fuer Biotechnologische Forschung (GBF), Braunschweig, Germany 		Jane Rogers
10 The Wellcome Trust Sanger Institute, Cambridge, UK
Genome Therapeutics Corporation (GTC), Waltham, MA, USA 		Jane Rogers
11 RIKEN Human Genome Research Group, Japan
The Broad Institute, Cambridge, MA USA 		Todd Taylor
12 Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA Steve Scherer
13 The Wellcome Trust Sanger Institute, Cambridge, UK 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 		Jean Weissenbach
15 The Broad Institute, Cambridge, MA USA
Institute of Molecular Biology (IMB),
Institute for Systems Biology (ISB), Seattle, WA 		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 		Jeremy Schmutz
17 The Broad Institute, Cambridge, MA USA Chad Nusbaum
18 The Broad Institute, Cambridge, MA USA
RIKEN Human Genome Research Group, Japan 		Chad Nusbaum
19 Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA
Stanford Human Genome Center, Palo Alto, CA, USA 		Jeremy Schmutz
20 The Wellcome Trust Sanger Institute, Cambridge, UK 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 		Todd Taylor
22 The Wellcome Trust Sanger Institute, Cambridge, UK
The University of Oklahoma, Norman, OK USA
Keio University School of Medicine, Tokyo, Japan 		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 		Jane Rogers
Y The Genome Institute at Washington University (WUSTL), St. Louis, MO USA Rick Wilson



  Alpaca Genome

The Alpaca Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Alpaca Genome Browser (vicPac2): Hiram Clawson and Luvina Guruvadoo
  • UCSC Alpaca Genome Browser (vicPac1): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Armadillo Genome

The Armadillo Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Armadillo Genome Browser (dasNov3): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Baboon Genome

The Baboon Genome Browser is provided by the Baboon Genome Sequencing Consortium with the following acknowledgments:

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.


  Bushbaby Genome

The Bushbaby Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Cat Genome

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:

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:

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:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Chimpanzee Genome

The UCSC Chimpanzee Genome Browsers display draft assembly data produced by the Chimpanzee Genome Sequencing Consortium:

  • 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 (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:
  • UCSC Chimp Genome Browser (panTro4): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • UCSC Chimp Genome Browser (panTro3): Hiram Clawson, Greg Roe, and Donna Karolchik
  • UCSC Chimp Genome Browser (panTro2): Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana Thakkapallayil, and Donna Karolchik
  • UCSC Chimp Genome Browser (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 in Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87. PMID: 16136131

The chimpanzee sequence is made freely available for public use by the Chimpanzee Genome Sequencing Consortium with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Chinese Hamster Genome

The Chinese hamster assembly was provided by the Beijing Genomics Institution-Shenzhen with the following acknowledgments:

The Chinese hamster sequence is made freely available by BGI with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Cow Genome

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:

  • 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 assembly is 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): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Chin Li, Hiram Clawson, Brian Raney and Steve Heitner.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Brian Raney, and Ann Zweig.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna Karolchik.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik.
Please acknowledge the appropriate institution when using these data sets. Citation information may be obtained from the UMD CBCB Bos taurus assembly page and the BCM-HGSC Bovine Genome Project page.


  Dog Genome

The UCSC Dog Genome Browser displays data from the July 2004 v1.0 (canFam1) and May 2005 v2.0 (canFam2) draft assemblies of the domestic dog (Canis familiaris). These assemblies are provided with the following acknowledgments:

The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite the following publication when using these data: Lindblad-Toh K et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438(7069):803-19. PMID: 16341006


  Dolphin Genome

The Dolphin Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Elephant Genome

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 (loxAfr3): Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik.
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The elephant sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Ferret Genome

The ferret assembly was provided by the Ferret Genome Sequencing Consortium with the following acknowledgments:

  • Sequencing/Assembly: Ferret Genome Sequencing Consortium and The Broad Institute, Cambridge, MA, USA
  • UCSC Ferret Genome Browser (musFur1): Hiram Clawson, Brian Lee, and Brooke Rhead
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The ferret sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Gibbon Genome

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:

The gibbon sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Gorilla Genome

The UCSC Gorilla Genome Browser displays the draft assembly of the gorilla genome (Gorilla gorilla gorilla) provided with the following acknowledgments:

The gorilla sequence is made freely available to the public by the Wellcome Trust Sanger Institute. Please review their data-sharing policy before using these data.


  Guinea Pig Genome

The UCSC Guinea Pig Genome Browser displays data from the Feb. 2008 CavPor3 draft assembly of the guinea pig (Cavia porcellus) from The Broad Institute. This assembly is provided with the following acknowledgments:

The guinea pig sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Hedgehog Genome

The Hedgehog Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute at MIT and Harvard, Cambridge, MA, USA
  • UCSC Hedgehog Genome Browser (eriEur2): Hiram Clawson, Brian Raney and Steve Heitner
  • UCSC Hedgehog Genome Browser (eriEur1): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Horse Genome

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:

The horse sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Kangaroo Rat Genome

The Kangaroo Rat Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Manatee Genome

The Manatee Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Manatee Genome Browser (triMan1): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The manatee genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Marmoset Genome

The Marmoset Genome Browser is provided with the following acknowledgments:

These data were produced by The Genome Institute at WUSTL and the BCM-HGSC and can be downloaded here.

The marmoset sequence is made freely available before scientific publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Megabat Genome

The Megabat (Fruitbat) Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Microbat Genome

The microbat (little brown bat) genome was provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Microbat Genome Browser (myoLuc2): Chin Li, Brian Raney, Robert Kuhn, Steve Heitner, Brooke Rhead, Greg Roe and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The microbat genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Minke whale Genome

The minke whale genome was provided by the Korea Ocean Research & Development Institute with the following acknowledgments:

The initial analyses of the minke whale genome can be found in 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

The minke whale genome sequence data are made available to the public with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Mouse Genome

The UCSC Mouse Genome Project is conducted in collaboration with the Mouse Sequencing Consortium and the Mouse Genome Sequencing Consortium. The mouse draft assembly displayed in the Genome Browser is assembled at NCBI.

The initial 3X coverage of the mouse genome was produced by the Mouse Sequencing Consortium, with the following acknowledgments:

Later releases of the assembly and map have been produced by the Mouse Genome Sequencing Consortium, with these acknowledgments:

Mouse genome sequence data are released weekly into a public repository maintained by EBI and NCBI. References to these data should cite the following publication: Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. PMID: 12466850

  Mouse Lemur Genome

The Mouse Lemur Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute at MIT and Harvard, Cambridge, MA, USA
  • UCSC Mouse Lemur Genome Browser (micMur1): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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<\p>

The mouse lemur data are provided with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Naked Mole-rat Genome

The naked mole-rat genome was provided with the following acknowledgments:

  • Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China
  • UCSC Naked Mole-rat Genome Browser (hetGla2): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • UCSC Naked Mole-rat Genome Browser (hetGla1): Chin Li and Luvina Guruvadoo
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The naked mole-rat genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Opossum Genome

The UCSC Opossum Genome Browser displays data from the draft assemblies of the opossum (Monodelphis domestica) produced by The Broad Institute. These assemblies are provided 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): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and Katrina Learned
  • UCSC Opossum Genome Browser/Initial Annotations (monDom4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik
  • UCSC Opossum Genome Browser/Initial Annotations (monDom1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik

The opossum sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Orangutan Genome

The UCSC Orangutan Genome Browser displays data from the draft assemblies of the Sumatran orangutan (Pongo pygmaeus abelii), which are provided with the following acknowledgments:

The orangutan sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Panda Genome

The panda assembly was provided by BGI-Shenzhen with the following acknowledgments:

The panda sequence is made freely available with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Pig Genome

The pig assembly was provided with the following acknowledgments:

The pig sequence is made freely available with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Pika Genome

The Pika Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Pika Genome Browser (ochPri2): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Platypus Genome

The platypus Genome Browser is provided with the following acknowledgments:

The platypus sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Rabbit Genome

The rabbit Genome Browser is provided with the following acknowledgments:

The rabbit sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Rat Genome

The UCSC Rat Genome Project is conducted in collaboration with the Rat Genome Sequencing Consortium.

The Rat Genome Browser is provided with the following acknowledgments:

The rat genome sequence is made freely available by the Rat Genome Project at the BCM-HGSC. Please cite the following publications when using these data:

Havlak, P. et al. The Atlas genome assembly system. Genome Res. 2004 Apr;14(4):721-32. PMID: 15060016; PMCID: PMC383319

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 data use limitations web page for restrictions on the use of these data.


  Rhesus Macaque Genome

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:

For more information on the MMGSC rhesus macaque genome project, see the BCM HGSC Rhesus Monkey Genome Project web page.

Additional acknowledgements:

  • UCSC Rhesus Genome Browser/Initial Annotations (rheMac3): 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
  • UCSC Rhesus Genome Browser/Initial Annotations (rheMac2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik.
  • UCSC Rhesus Genome Browser/Initial Annotations (rheMac1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Robert Baertsch, Galt Barber, and Donna Karolchik.

The initial sequencing and analysis of the rhesus macaque genome produced by the MMGSC was published by the Rhesus Macaque Genome Sequencing and Analysis Consortium in 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 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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. 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.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Rock Hyrax Genome

The Rock Hyrax Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Sheep Genome

The sheep (Ovis aries) assembly was provided by the International Sheep Genomics Consortium (ISGC) sequencing center with the following acknowledgments:

The sheep sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Shrew Genome

The Common Shrew Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Sloth Genome

The Sloth Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Squirrel Genome

The Squirrel Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Genome Browser (speTri2): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Squirrel Monkey Genome

The Squirrel Monkey Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Monkey Genome Browser (saiBol1): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The squirrel monkey genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Tarsier Genome

The Tarsier Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Tasmanian Devil Genome

The Tasmanian Devil assembly was provided with the following acknowledgments:

The Tasmanian devil sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Tenrec Genome

The tenrec genome was provided by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Tenrec Genome Browser (echTel2): Hiram Clawson, Brian Raney and Steve Heitner
  • UCSC Tenrec Genome Browser (echTel1): Hiram Clawson, Brian Raney and Steve Heitner
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The tenrec genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Tree Shrew Genome

The Tree Shrew Genome Browser is provided with the following acknowledgments:

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:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Wallaby Genome

The wallaby Genome Browser was provided with the following acknowledgments:

The wallaby sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  White Rhinoceros Genome

The southern white rhinoceros Genome Browser 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 (cerSim1): Hiram Clawson and Steve Heitner
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The southern white rhinoceros sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  American Alligator Genome

The American alligator assembly was provided by the International Crocodilian Genomes Working Group with the following acknowledgments:

The American alligator sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (International Crocodilian Genomes Working Group) is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Atlantic Cod Genome

The Atlantic Cod Genome Browser is provided with the following acknowledgments:

The initial analyses of the Atlantic cod dataset can be found in Johansen SD et al. Large-scale sequence analyses of Atlantic cod. N Biotechnol. 2009 Jun;25(5):263-71. PMID: 19491044

The Atlantic cod sequence is made freely available with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Budgerigar Genome

The Budgerigar Genome Browser is provided with the following acknowledgments:

The budgerigar sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Chicken Genome

The Chicken Genome Browser 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 (galGal4): Hiram Clawson, Brian Raney and Steve Heitner
  • UCSC Chicken Genome Browser (galGal3): Angie Hinrichs, Kayla Smith, Donna Karolchik
  • UCSC Chicken Genome Browser (galGal2): Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik

The chicken sequence is made freely available to the community by The Genome Institute at WUSTL with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly cited:
    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
  3. Any redistribution of the data should carry this notice.

The BGI gene annotations and SNP data are made available with the following terms of use:

  1. Users are free to use these data in scientific papers analyzing particular genes, if the Beijing Genomics Institute (BGI) is acknowledged.
  2. 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.
  3. Any redistribution of these data should carry this notice.

  Coelacanth Genome

The Coelacanth Genome Browser is provided with the following acknowledgments:

The initial sequencing and analysis of the coelacanth genome can be found in Amemiya CT et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6. PMID: 23598338; PMCID: PMC3633110

The coelacanth sequence is made freely available to the community by The Broad Institute with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing these data if the provider of these data is properly acknowledged.
  3. The center producing the data (The Broad Institute) 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Elephant Shark Genome

The elephant shark assembly was provided by the Singapore Institute of Molecular and Cell Biology with the following acknowledgments:

The initial analysis of the elephant shark genome can be found in 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; PMC: PMC3964593

The elephant shark sequence is made freely available by ICMB with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  Fugu Genome

The Fugu whole genome shotgun assembly was provided by the U.S. DOE 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 (fr3): Hiram Clawson and Greg Roe
  • UCSC Fugu Genome Browser (fr2): Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik
  • UCSC Fugu Genome Browser (fr1): Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The Fugu sequence data have been freely provided by the JGI for use in the UCSC Genome Browser. Please see the JGI data release policy for restrictions regarding the use of these data.


  Lamprey Genome

The lamprey assembly was provided by The Genome Institute at Washington University (WUSTL) with the following acknowledgments:

The lamprey sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Lizard Genome

The lizard assembly was provided by the Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
  • UCSC Lizard Genome Browser (anoCar2): Hiram Clawson, Brian Raney, Luvina Guruvadoo, and Donna Karolchik
  • UCSC Lizard Genome Browser (anoCar1): Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The lizard sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Medaka Genome

The Medaka whole genome shotgun assembly was 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 (oryLat2): Hiram Clawson, Pauline Fujita, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The Medaka genome sequence data are made available to the public with certain restrictions.


  Medium Ground Finch Genome

The initial medium ground finch genome assembly is the product of a collaboration between the Genome 10K Project and Beijing Genomics Institute (BGI). The Medium Ground Finch Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: Genome 10K Project and Beijing Genomics Institute (BGI)
  • UCSC Medium Ground Finch Genome Browser (geoFor1): Hiram Clawson and Greg Roe
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The medium ground finch sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Nile Tilapia Genome

The Nile Tilapia Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Nile Tilapia Genome Browser (oreNil2): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The Nile Tilapia genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Painted Turtle Genome

The Painted Turtle Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly: International Painted Turtle Genome Sequencing Consortium
  • UCSC Painted Turtle Genome Browser (chrPic1): Hiram Clawson, Brian Raney and Steve Heitner
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The painted turtle genome sequence data are made available to the public with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Stickleback Genome

The stickleback assembly was provided by the Broad Institute with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
  • UCSC Stickleback Genome Browser (gasAcu1): Angie Hinrichs, Hiram Clawson, Kayla Smith, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The stickleback sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  Tetraodon Genome

The Tetraodon nigroviridis assemblies have been provided with the following acknowledgments:

These data have been freely provided by Genoscope before publication for use in the UCSC Genome Browser with the following understanding
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Genoscope reserves the right to publish the initial large-scale analyses of the dataset, 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 magnitude of a Tetraodon chromosome (that is, 5 Mb or more).

  Turkey Genome

The turkey Genome Browser was provided with the following acknowledgments:

The turkey sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Any redistribution of the data should carry this notice.


  X. tropicalis Genome

The X. tropicalis draft assemblies were provided by the U.S. DOE Joint Genome Institute (JGI). These assemblies have the following acknowledgments:

  • Sequencing/Assembly: JGI, Walnut Creek, CA, USA
  • UCSC X. tropicalis Genome Browser (xenTro3): Hiram Clawson, Brian Raney, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik
  • UCSC X. tropicalis Genome Browser (xenTro2): Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik
  • UCSC X. tropicalis Genome Browser (xenTro1): Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik
  • Initial Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

These sequence data are made freely available by the JGI. Please refer to the JGI data release policy for data use guidelines.

  Zebra Finch Genome

The zebra finch draft assembly was obtained from 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 (taeGut2): Hiram Clawson, Brian Raney, and Steve Heitner
  • UCSC Zebra Finch Genome Browser (taeGut1): Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik
  • Initial Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The zebra finch sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Zebrafish Genome

The zebrafish draft assemblies were provided by The Wellcome Trust Sanger Institute. The UCSC Zebrafish Genome Browser has 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
  • Initial Annotations:
  • UCSC Zebrafish Genome Browser (danRer7): Hiram Clawson, Mary Goldman, Greg Roe, Brian Raney, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer6): Galt Barber, Robert Kuhn, Katrina Learned, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer5): Rachel Harte, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer4): Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer3): Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer2): Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson

Sequencing and analysis of the zebrafish genome was published by Howe K et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 25;496(7446):498-503. PMID: 23594743

These sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained directly from ftp://ftp.sanger.ac.uk/pub/zebrafish/. Please adhere to the data use guidelines for these data.

For more information about the assemblies, see the Sanger Institute's Danio rerio Sequencing Project web page.


  C. intestinalis Genome

The C. intestinalis v1.0 and v2.0 draft assemblies were provided by the U.S. DOE Joint Genome Institute (JGI). These assemblies have the following acknowledgments, as listed on the JGI website:

The sequence data have been freely provided by the JGI for use in the UCSC Genome Browser. The JGI Data Release Policy outlines restrictions on the use of these data. For more information about the C. intestinalis assembly, see the JGI Ciona web page.


  Lancelet Genome

The lancelet assembly was provided by the DOE 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 (braFlo1): Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The lancelet sequence is made freely available before scientific publication by the JGI. Please see the JGI data release policy for usage restrictions and citation information.


  S. purpuratus Genome

The UCSC S. purpuratus Genome Browser displays data obtained from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). The Sep. 2006 draft assembly shows data from Baylor version Spur 2.1; the Apr. 2005 assembly corresponds to Baylor version Spur_0.5. These data are provided with the following acknowledgments:

For more information on the S. purpuratus genome project, see the BCM-HGSC Sea Urchin Genome Project web page.

To review the conditions for use regarding these data, see the BCM-HGSC Conditions for Use web page.

  A. gambiae Genome

The MOZ2 A. gambiae data were provided by The International Anopheles Genome Project and downloaded from Ensembl. The data have the following acknowledgments:

The A. gambaie sequence is made freely available by The International Anopheles Genome Project.

  A. mellifera Genome

The Amel_1.2 data were provided by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) with the following acknowledgments:

The A. mellifera sequence is made freely available before scientific publication by the BCM-HGSC. See the Baylor conditions of use statement for guidelines regarding the use of these data.

  D. ananassae Genome

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

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. erecta Genome
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

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. grimshawi Genome
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

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. melanogaster Genome

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 (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.

  D. mojavensis Genome

These data were produced by Agencourt Bioscience. The D. mojavensis Genome Browser has the following acknowledgments:

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. persimilis Genome

The droPer1 assembly was provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC D. persimilis Genome Browser (droPer1): Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The D. persimilis sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  D. pseudoobscura Genome

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
  • UCSC D. pseudoobscura Genome Browser (dp3): Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik
  • UCSC D. pseudoobscura Genome Browser (dp2): Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna Karolchik
  • 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.


  D. sechellia Genome

The droSec1 assembly was provided with the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
  • UCSC D. sechellia Genome Browser (droSec1): Angie Hinrichs, Kayla Smith and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The D. sechellia sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  D. simulans Genome

These data were provided with the following acknowledgments:

The D. simulans sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  D. virilis Genome

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
  • Funding: National Human Genome Research Institute (NHGRI), USA
  • UCSC D. virilis Genome Browser (droVir2): Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik
  • UCSC D. virilis Genome Browser (droVir1): Angie Hinrichs, Brian Raney, Heather Trumbower, Robert Kuhn, Jennifer Jackson, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

These data have been freely provided by Agencourt Bioscience before publication for use in the UCSC Genome Browser with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

  D. yakuba Genome

These data were provided by The Genome Institute at Washington University (WUSTL) with the following acknowledgments:

The D. yakuba sequence is made freely available before scientific publication by The Genome Institute at WUSTL with the following understanding:

  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. The Drosophila yakuba analysis group is aiming to publish an initial analysis of the D. yakuba genome sequence in 2005 (submitted in early 2005) that will include descriptions of the assembly, genome landscape, comparative analysis and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson, Genome Sequencing Center Director, Washington University School of Medicine. We welcome a coordinated approach to describing this community resource.
  4. Any redistribution of the data should carry this notice.

  C. elegans Genome

The C. elegans data was obtained from WormBase. We'd like to thank The Genome Institute at Washington University (WUSTL) and the Sanger Institute for their collaborative work on sequencing the C. elegans genome, and the WormBase consortium for providing access to the current C. elegans sequence.


  Worm Genomes (other than C. elegans)

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 before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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.
  4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.


  Yeast Genome

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 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 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 ftp://genome-ftp.stanford.edu/pub/yeast/data_download. 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.


  California Sea Hare Genome

The Aplysia californica genome assembly has the following acknowledgments:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC California Sea Hare (aplCal1) Genome Browser: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

The California sea hare sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
  3. 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).
  4. Any redistribution of the data should carry this notice.


  External Contributors to the UCSC Genome Browser Project

  Acknowledgment of Early Support

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. 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, 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.