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

• Human Genome
• Alpaca Genome
• Armadillo Genome
• Baboon Genome
• Bushbaby Genome
• Cat Genome
• Chimpanzee Genome
• Chinese Hamster Genome
• Cow Genome
• Dog Genome
• Dolphin Genome
• Elephant Genome
• Ferret Genome
• Gibbon Genome
• Gorilla Genome
• Guinea Pig Genome
• Hedgehog Genome
• Horse Genome
• Kangaroo Rat Genome
• Manatee Genome
• Marmoset Genome
• Megabat Genome
• Microbat Genome
• Minke Whale Genome
• Mouse Genome
• Mouse Lemur Genome
• Naked Mole-rat Genome
• Opossum Genome
• Orangutan Genome
• Panda Genome
• Pig Genome
• Pika Genome
• Platypus Genome
• Rabbit Genome
• Rat Genome
• Rhesus Genome
• Rock Hyrax Genome
• Sheep Genome
• Shrew Genome
• Sloth Genome
• Squirrel Genome
• Squirrel Monkey Genome
• Tarsier Genome
• Tasmanian Devil Genome
• Tenrec Genome
• Tree Shrew Genome
• Wallaby Genome
• White Rhinoceros Genome

Other Vertebrates

• American Alligator Genome
• Atlantic Cod Genome
• Budgerigar Genome
• Chicken Genome
• Coelacanth Genome
• Elephant Shark Genome
• Fugu Genome
• Lamprey Genome
• Lizard Genome
• Medaka Genome
• Medium Ground Finch Genome
• Nile Tilapia Genome
• Painted Turtle Genome
• Stickleback Genome
• Tetraodon Genome
• Turkey Genome
• X. tropicalis Genome
• Zebra Finch Genome
• Zebrafish Genome

Deuterostomes

• C. intestinalis Genome
• Lancelet Genome
• S. purpuratus Genome

Insects

• A. gambiae Genome
• A. mellifera Genome
• D. ananassae Genome
• D. erecta Genome
• D. grimshawi Genome
• D. melanogaster Genome
• D. mojavensis Genome
• D. persimilis Genome
• D. pseudoobscura Genome
• D. sechellia Genome
• D. simulans Genome
• D. virilis Genome
• D. yakuba Genome

Nematodes

• C. brenneri Genome
• C. briggsae Genome
• C. elegans Genome
• C. japonica Genome
• C. remanei Genome
• P. pacificus Genome

Other

• Yeast Genome
• California Sea Hare Genome

• Ebola Genome

• Other scientists featured on this site
• Acknowledgment of early support
• UCSC Genome Browser project team

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.

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

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

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 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.

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 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.

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

• Funding: National Human Genome Research Institute (NHGRI), USA
• Sequencing/Assembly: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• UCSC Baboon Genome Browser (papAnu2): Chin Li and Luvina Guruvadoo
• UCSC Baboon Genome Browser (papHam1): 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 Bushbaby Genome Browser is provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Bushbaby Genome Browser (otoGar3): 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 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.

The UCSC felCat5 Genome Browser displays data from the Sep. 2011 Felis_catus-6.2 assembly of the domestic cat produced by the International Cat Genome Sequencing Consortium. This assembly was provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI), Bethesda, MD
  
• 454 Production sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
• BAC sequencing: The Genome Institute at WUSTL
• Plasmid and fosmid sequencing: The Broad Institute, Cambridge, MA, USA and Agencourt Bioscience
• Sequence assembly and data integration for creation of chromosomal AGP files: The Genome Institute at WUSTL
• Whole genome alignments: Brian Raney, UCSC Genome Browser Group, University of California, Santa Cruz, CA, and The Genome Institute at WUSTL
• Cat RH map: Bill Murphy, Texas A&M University, College Station, TX.
• DNA source: Dr. Kristina Narfstrom, University of Missouri, Columbia, MO.
• UCSC Cat Genome Browser/Initial Annotations (felCat5): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik

The UCSC felCat4 Genome Browser displays data from the Dec. 2008 catChrV17e draft assembly, based on sequence reads from six domestic cats and one wild cat. The browser is provided with the following acknowledgments:

• Sequencing/Assembly:
  • NHGRI Genome Technology Branch and NIH Intramural Sequencing Center, Bethesda, MD, USA
  • Agencourt Bioscience, Danvers, MA, USA
  • NCI Laboratory of Genomic Diversity, Frederick, MD, USA
  • Hill's Pet Nutrition, Inc., Topeka, KS, USA
• UCSC Cat Genome Browser/Initial Annotations (felCat4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Chin Li, Hiram Clawson, Antonio Coelho, Mary Goldman, and Donna Karolchik

The UCSC felCat3 Genome Browser displays data from the March 2006 v3 draft assembly of the domestic cat (Felis catus). This assembly was provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI), Bethesda, MD
  
• Project Leadership: The Broad Institute, Cambridge, MA, USA
• Sequencing/Assembly: The Broad Institute - team led by by Kerstin Lindblad-Toh, Ph.D.
• Plasmid and fosmid libraries: The Broad Institute
• BAC end sequencing: Agencourt Bioscience, Danvers, MA, USA
  
• UCSC Cat Genome Browser/Initial Annotations (felCat3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil

The catChrV17e cat assembly was initially published in Pontius JU et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 2007 Nov;17(11):1675-89. PMID 17975172; PMCID: PMC2045150

The Broad Institute released the initial 2X (v3) assembly of the cat genome as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The cat sequence is made freely available with the following understanding:

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
  
• Sequencing/Assembly (panTro2, panTro3, panTro4):
  • Whole genome shotgun (WGS) sequence data assembly and organization: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
  • Underlying WGS data: The Genome Institute at WUSTL and The Broad Institute, Cambridge, MA USA
  • 5-Mb region of chromosome 7 at chr7:84674857-89461887): finished by The Genome Institute at WUSTL
  • Chromosome Y sequence: finished by The Genome Institute at WUSTL, with detailed mapping and extensive collaboration with David Page's group at the Whitehead Institute. For more information, see:
    • Hughes JF et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature. 2005 Sep 1;437(7055):100-3. PMID: 16136134
    • "The DNA Sequence of Chimpanzee Chromosome Y", unpublished.
  • Chromosome 21 sequence: Todd Taylor and the RIKEN Genomic Sciences Center. See Watanabe et al. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004 May 27;429(6990):382-8. PMID: 15164055
• 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:
  • The Genome Institute at WUSTL, St. Louis, MO, USA
  • Research Group on Biomedical Informatics of IMIM/UPF (GRIB), Barcelona, Spain
  • Riken Genomic Sciences Center, Yokohama City, Japan
  • UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA
• 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 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.

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

• Sequencing/Assembly: Beijing Genomics Institution-Shenzhen
• UCSC Chinese Hamster Genome Browser (criGri1): Hiram Clawson, Brian Raney, and Steve Heitner.
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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:

• Genome sequence: NCBI Trace Archive
• Genome assembly: University of Maryland Center for Bioinformatics and Computational Biology, College Park, MD, USA
• UCSC Cow Genome Browser/Initial Annotations (bosTau8): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Steve Heitner and Luvina Guruvadoo
• UCSC Cow Genome Browser/Initial Annotations (bosTau6): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Chin Li, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik

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.

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:

• Funding: The National Human Genome Research Institute
  
• Project Leadership: The Broad Institute, Cambridge, MA, USA
• Sequencing/Assembly: The Broad Institute - team led by by Kerstin Lindblad-Toh, Ph.D.
• Plasmid and fosmid libraries: The Broad Institute
• BAC libraries: Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
• BAC end sequencing: Agencourt Bioscience, Danvers, MA, USA
• RH map: Centre National de la Recherche Scientifique (CNRS), France
• FISH mapping: North Carolina State University (NCSU), Raleigh, NC, USA
  
• Dog Selection: Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
• UCSC Dog Genome Browser/Initial Annotations (canFam3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson and Luvina Guruvadoo
• UCSC Dog Genome Browser/Initial Annotations (canFam2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Angie Hinrichs, Jennifer Jackson, and Donna Karolchik
• UCSC Dog Genome Browser/Initial Annotations (canFam1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Angie Hinrichs, Robert Kuhn and Donna Karolchik

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

The Dolphin Genome Browser is provided with the following acknowledgments:

• Sequencing: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Dolphin Genome Browser (turTru2): 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 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.

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

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.

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

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.

The UCSC Gibbon Genome Browser displays data from the draft assemblies of the northern white-cheeked gibbon (Nomascus leucogenys) provided by the Gibbon Genome Sequencing Consortium with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly:
  • The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• UCSC Gibbon Genome Browser (nomLeu3): Pauline Fujita and Hiram Clawson
• UCSC Gibbon Genome Browser (nomLeu2): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
• UCSC Gibbon Genome Browser (nomLeu1): Chin Li, Brooke Rhead, Steve Heitner, Lauren Scott and Donna Karolchik
• Initial Annotations: UCSC Genome Bioinformatics Group

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.

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

• Sequencing: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
• Assembly:
  • The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
  • The European Bioinformatics Institute (EBI), Hinxton, Cambridge, UK
• UCSC Gorilla Genome Browser/Initial Annotations (gorGor3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Mark Diekhans, Brian Raney, Brooke Rhead, Steve Heitner, Lauren Scott and Donna Karolchik

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:

• Funding: The National Human Genome Research Institute
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Guinea Pig Genome Browser/Initial Annotations (cavPor3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith, Robert Kuhn, and Donna Karolchik.

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.

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 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.

The UCSC Horse Genome Browser displays the draft assembly of the horse (Equus caballus) genome from The Broad Institute. This assembly is provided with the following acknowledgments:

• Funding: The National Human Genome Research Institute
• Project Leadership: The Broad Institute, Cambridge, MA, USA
• Sequencing/Assembly: The Broad Institute
• BAC End Reads: University of Veterinary Medicine Hanover, Germany, and the Helmholtz Centre for Infection Research, Braunschweig, Germany
• UCSC Horse Genome Browser/Initial Annotations (equCab2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna Karolchik
• UCSC Horse Genome Browser/Initial Annotations (equCab1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate Rosenbloom, and Donna Karolchik

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.

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

• Sequencing: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Kangaroo Rat Genome Browser (dipOrd1): 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 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.

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

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.

The Marmoset Genome Browser is provided with the following acknowledgments:

• Sequencing and assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA and Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• DNA Source: Dr. Suzette Tardif, Southwest National Primate Research Center, San Antonio, TX, USA
• CHORI-259 BAC library: Dr. Pieter DeJong, Children's Hospital Oakland Research Institute, Oakland, CA, USA
• UCSC Marmoset Genome Browser (calJac3): Hiram Clawson, Chin Li, Mark Diekhans, Mary Goldman, Vanessa Swing, and Donna Karolchik
• UCSC Marmoset Genome Browser (calJac1): Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly:
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
  • The Broad Institute, Cambridge, MA, USA
• UCSC Megabat Genome Browser (pteVam1): 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 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.

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

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.

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

• Sequencing/Assembly: Korea Ocean Research & Development Institute, Ansan, Gyeonggi-do, South Korea
• UCSC Minke whale Genome Browser (balAcu1): Hiram Clawsom and Matthew Speir
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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.

• Project Oversight: Arthur Holden and Francis Collins
• Funding:
  • GlaxoSmithKline
  • Merck Genome Research Institute
  • Affymetrix, Inc.
  • The Wellcome Trust
  • The National Institutes of Health
• Sequencing:
  • The Broad Institute, Cambridge, MA, USA
  • The Genome Institute at Washington University (WUSTL)
  • The Wellcome Trust Sanger Institute

• Funding:
  • National Institutes of Health
  • The Wellcome Trust
  • GlaxoSmithKline
  • The Merck Genome Research Institute
  • Affymetrix
• Sequencing:
  • The Broad Institute's Arachne Group
  • The Wellcome Trust Sanger Institute
  • The Genome Institute at Washington University (WUSTL)
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)
  • Wolfson Institute for Biomedical Research
  • University of Oklahoma, Advanced Center for Genome Technology
  • UK MRC Mouse Genome Centre and Mammalian Genetics Unit
  • National Institutes of Health Intramural Sequencing Center
  • Harvard Partners Genome Center
  • Cold Springs Harbor Laboratory
• Physical Map:
  • Mouse BAC libraries: Children's Hospital Oakland Research Institute (CHORI)
  • BAC fingerprint map: Genome Sciences Centre
  • BAC end sequences: The Institute of Genome Research (TIGR)
  • TPF production - Tina Graves, April Cook, Christine Burton, Darren Graham, Shannon Dugan, Donna Muzny
• Assembly: Deanna Church, Richa Agarwala, Josh Cherry, Mike DiCuccio, Hsiu-Chuan Chen, Paul Kitts, Victor Sapojnikov
• cDNA Sequencing:
  • Riken Institute
  • The Mammalian Gene Collection
• UCSC Mouse Genome Browser (mm10): Hiram Clawson and Luvina Guruvadoo
• UCSC Mouse Genome Browser (mm9): Hiram Clawson, Archana Thakkapallayil, Robert Kuhn and Donna Karolchik
• UCSC Mouse Genome Browser (mm8): Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead, Archana Thakkapallayil, and Donna Karolchik
• UCSC Mouse Genome Browser (mm7): Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik
• UCSC Mouse Genome Browser (mm6): Hiram Clawson, Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali Sultan-Qurraie, Heather Trumbower and Donna Karolchik
• Annotations:
  • UCSC Genome Bioinformatics Group
  • The Jackson Laboratory
  • NCBI
  • Ensembl
  • Pennsylvania State University
  • University of California Berkeley/LBNL

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 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.

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

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.

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

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.

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:

• Sequencing:
  • The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
• Sequence Assembly and Chromosomal Sequence/AGP Construction: The Genome Institute at WUSTL
• DNA Source: Dr. Greely Stones - Gladys Porter Zoo, Brownsville, TX, USA
• BAC Library: Yuko Yoshonaga in Pieter de Jong's laboratory - Children's Hospital Oakland Research Institute, Oakland, CA, USA
• Fosmid Library: The Genome Institute at WUSTL
• Fingerprint Map: The Genome Institute at WUSTL
• Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses: Mariano Rocchi - Department of Genetics and Microbiology, University of Bari, Bari, Italy
• Fosmid End Placement against the Human Genome (used for breakpoint/inversion analyses during AGP construction): Lin Chen, Evan Eichler - Department of Genome Sciences, University of Washington, Seattle, WA, USA
• Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH)
• UCSC Orangutan Genome Browser/Initial Annotations (ponAbe2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik

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.

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

• Sequencing/Assembly: The Beijing Genomics Institute at Shenzhen
• UCSC Panda Genome Browser (ailMel1): Hiram Clawson, Ann Zweig, and Antonio Coelho.
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

The pig assembly was provided with the following acknowledgments:

• Sequencing/Assembly:
  • The Swine Genome Sequencing Consortium
  • Wellcome Trust Sanger Institute
• UCSC Pig Genome Browser (susScr3): Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
• UCSC Pig Genome Browser (susScr2): Hiram Clawson, Brian Raney, Mark Diekhans, and Mary Goldman.
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

The Pika Genome Browser is provided with the following acknowledgments:

• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Pika Genome Browser (ochPri3): Hiram Clawson, Brian Raney, and Steve Heitner
• 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 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.

The platypus Genome Browser is provided with the following acknowledgments:

• Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
• UCSC Platypus Genome Browser (ornAna1): Angie Hinrichs, Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

The rabbit Genome Browser is provided with the following acknowledgments:

• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Rabbit Genome Browser (oryCun2): Hiram Clawson and Antonio Coelho
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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:

• Project Coordination: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Richard Gibbs, Director
• Funding:
  • National Human Genome Research Institute (NIH)
  • National Heart, Lung and Blood Institute (NIH)
• Sequencing:
  • BCM-HGSC
  • Celera Genomics Group of Applera Corporation
  • Genome Therapeutics Corporation
  • The University of Utah
• Assembly: BCM-HGSC ATLAS group - Rui Chen, James Durbin, Paul Havlak
• Fingerprint Mapping: The British Columbia Cancer Agency Genome Sciences Center - Marco Marra, Jackie Schein
• BAC End Sequencing: The Institute for Genomic Research - Shaying Zhao
• BAC Library Construction and Distribution: Children's Hospital Oakland Research Institute (CHORI) - Pieter deJong
• Rat Genome Database: Medical College of Wisconsin
• UCSC Rat Genome Browser (rn6) - Hiram Clawson, Brian Raney and Matthew Speir
• UCSC Rat Genome Browser (rn5) - Hiram Clawson, Brian Raney and Steve Heitner
• UCSC Rat Genome Browser (rn4) - Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik
• UCSC Rat Genome Browser (rn3) - Hiram Clawson, Heather Trumbower, Robert Kuhn, Yontao Lu, Terry Furey, Mark Diekhans, Robert Baertsch, Donna Karolchik, and Jim Kent

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.

The UCSC Genome Browser displays multiple assemblies of the Rhesus macaque genome produced by different institutions:

• rheMac3 Genome Browser: Oct. 2010 draft assembly of the rhesus monkey, version CR_1.0 from Beijing Genomics Institute-Shenzhen (BGI), Shenzhen, China
• rheMac2 Genome Browser: Jan. 2006 draft assembly of the rhesus monkey, version Mmul_051212 from the Macaca mulatta Genome Sequencing Consortium (MMGSC) led by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), in collaboration with the J. Craig Venter Science Foundation Joint Technology Center and The Genome Institute at Washington University (WUSTL)
• rheMac1 Genome Browser: Jan. 2005 draft assembly of the rhesus monkey, version Mmul_0.1 from MMGSC (see above)

The BGI assembly is provided with the following acknowledgments:

• Funding: Southern China Center for Innovative Pharmaceuticals (SCCIP), the National Natural Science Foundation of China, the Shenzhen Municipal Government of China, the Major State Basic Research Development Program of China, the National Basic Research Program of China, and the National Science and Technology Major Project of Key Drug Innovation and Development
• Sequencing/Assembly: BGI, Shenzhen, China

The MMGSC assembly is provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI), USA
• Sequencing/Assembly: BCM-HGSC, Houston, TX, USA in collaboration with:
  • J. Craig Venter Science Foundation Joint Technology Center, Rockville, MD, USA
  • The Genome Institute at WUSTL, St. Louis, MO, USA
• BAC resources: Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
• BAC-based fingerprint map: Genome Sciences Centre, Vancouver, B.C.

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

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 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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly:
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
  • The Broad Institute, Cambridge, MA, USA
• UCSC Rock Hyrax Genome Browser (proCap1): 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 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.

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

• Sequencing/Assembly: International Sheep Genomics Consortium (ISGC) sequencing center
• Mitochondrial Genome Sequencing: Justus-Liebig-University
• UCSC Sheep Genome Browser (oviAri3): Hiram Clawson, Brian Raney, Matthew Speir, Brian Lee, Brooke Rhead, Steve Heitner, and Donna Karolchik
• UCSC Sheep Genome Browser (oviAri1): Chin Li, Greg Roe, and Luvina Guruvadoo
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Shrew Genome Browser (sorAra2): Hiram Clawson, Brian Raney, and Steve Heitner
• UCSC Shrew Genome Browser (sorAra1): 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 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.

The Sloth Genome Browser is provided with the following acknowledgments:

• Sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
• Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Sloth Genome Browser (choHof1): 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 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.

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 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.

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

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.

The Tarsier Genome Browser is provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly:
  • Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Houston, TX, USA
  • The Broad Institute, Cambridge, MA, USA
• UCSC Tarsier Genome Browser (tarSyr1): 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 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.

The Tasmanian Devil assembly was provided with the following acknowledgments:

• Sequencing/Assembly: Wellcome Trust Sanger Institute, Cambridge, UK
• UCSC Tasmanian Devil Genome Browser (sarHar1): Chin Li and Luvina Guruvadoo
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Tree Shrew Genome Browser (tupBel1): 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 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.

The wallaby Genome Browser was provided with the following acknowledgments:

• Sequencing/Assembly: The Tammar Wallaby Genome Sequencing Consortium - Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and the Australian Genome Research Facility
• UCSC Wallaby Genome Browser (macEug2): Chin Li and Luvina Guruvadoo
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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.

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

• Sequencing/Assembly: International Crocodilian Genomes Working Group
• UCSC American Alligator Genome Browser (allMis1): Hiram Clawson, Jonathan Casper, and Brian Lee
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Funding: Research Council of Norway (FUGE)
• Sequencing/Assembly: GenoFisk Consortium
• UCSC Atlantic Cod Genome Browser (gadMor1): 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 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.

The Budgerigar Genome Browser is provided with the following acknowledgments:

• Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
• UCSC Budgerigar Genome Browser (melUnd1): 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

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.

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:
  • NIH Intramural Sequencing Center (NISC) (AC091708.2, AC094012.2, AC138565.3)
  • S. Kerje and L. Andersson, Uppsala University (AY636124.1)
  • The Genome Institute at WUSTL (all others)
• 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

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.

The Coelacanth Genome Browser is provided with the following acknowledgments:

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Coelacanth Genome Browser (latCha1): 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 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.

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

• Sequencing/Assembly: Singapore Institute of Molecular and Cell Biology
• UCSC Elephant Shark Genome Browser (calMil1): Hiram Clawson, Jonathan Casper, and Donna Karolchik.
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly:
  • The Genome Institute at WUSTL, St. Louis, MO, USA
  • Jeramiah Smith (University of Kentucky, University of Washington Department of Genome Sciences, and Benaroya Research Institute at Virginia Mason)
• UCSC Lamprey Genome Browser (petMar2): Hiram Clawson, Brian Raney, and Steve Heitner
• UCSC Lamprey Genome Browser (petMar1): Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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.

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 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

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.

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

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.

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

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.

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

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.

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

• Sequencing/Assembly:
  • Genoscope, Evry, France
  • The Broad Institute,MA, USA
• Project Funding:
  • Consortium National de Recherche en Genomique, France
  • National Human Genome Research Institute (NHGRI), USA
• Initial Genome Browser Annotations:
  • Genoscope - Genscan gene predictions, GAZE gene predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - remaining annotations (based on data from Genoscope)
• UCSC Tetraodon Genome Browser (tetNig2): Hiram Clawson, Mark Diekhans, Brian Raney, Ann Zweig, Mary Goldman, Vanessa Swing, Antonio Coelho, Robert Kuhn, and Donna Karolchik
• UCSC Tetraodon Genome Browser (tetNig1): Rachel Harte, Robert Kuhn, Donna Karolchik

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).

The turkey Genome Browser was provided with the following acknowledgments:

• Sequencing/Assembly: The Turkey Genome Consortium - Virginia Tech College of Agriculture and Life Sciences and Virginia Bioinformatics Institute, Blacksburg, VA, USA
• UCSC Turkey Genome Browser (melGal1): Chin Li, Mark Diekhans, Brian Raney, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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

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.

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:
  • The Wellcome Trust Sanger Institute, UK
  • Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands
  • Max-Planck Institute for Developmental Biology, Germany
• 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:
  • Yi Zhou, Anthony DiBiase, Leonard Zon and the Zebrafish Genome Initiative at Boston Children's Hospital, Boston, MA, US - collaboration on Zebrafish WZ EST clusters, BAC End Singles/Pairs, Radiation Hybrid, and Human tBLASTn annotation tracks.
  • Washington University in St. Louis, St. Louis, MO, US - Zebrafish WZ EST clusters data
  • Ensembl, UK - Ensembl gene predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations
• UCSC Zebrafish Genome 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

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.

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:

• Project Funding: Work performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.
• Project Collaborators:
  • JGI, Walnut Creek, CA, USA
  • Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
  • Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA
  • National Institute of Genetics, Mishima, Japan
  • Oak Ridge National Laboratory, Oak Ridge, TN, USA
  • Los Alamos National Laboratory, Los Alamos, NM, USA
• Annotations:
  • Colin Dewey, University of California, Berkeley, CA, USA - SNAP Gene Predictions, using the SNAP parser written by Ian Korf
  • JGI, Walnut Creek, CA, USA - JGI Gene Predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations
• UCSC C. intestinalis Genome Browser (ci2): Brian Raney, Mark Diekhans, Ann Zweig, Kayla Smith, Robert Kuhn, Donna Karolchik
• UCSC C. intestinalis Genome Browser (ci1): Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik

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 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:

• Funding - National Human Genome Research Institute (NHGRI)
• Sequencing/Assembly: BCM-HGSC, Houston, TX, USA
  
• UCSC S. purpuratus Genome Browser/Initial Annotations (strPur2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Kord Kober, Heather Trumbower, Rachel Harte, Kayla Smith and Donna Karolchik.
• UCSC S. purpuratus Genome Browser/Initial Annotations (strPur1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Andy Pohl, Kayla Smith and Donna Karolchik.

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

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

• Funding: National Institute of Allergy and Infectious Diseases (NIAID), French Ministry of Research, and the World Health Organization (WHO). Celera Genomics and Genoscope were funded respectively by National Institutes of Health (NIH) and French Ministry of Research.
• Project collaboration: The International Anopheles Genome Project - a collaboration between Celera Genomics, Genoscope, University of Notre Dame, EBI/Sanger Institute, EMBL, Institut Pasteur, The Institute of Molecular Biology and Biotechnology (IMBB) and The Institute for Genomic Research (TIGR).
• Sequencing and Assembly: Celera Genomics, Genoscope
• Data Downloads: Ensembl
• UCSC A. gambaie Genome Browser (anoGam1): Angie Hinrichs, Galt Barber and Donna Karolchik
• Initial Genome Browser Annotations: Ensembl and Celera Genomics (Ensembl Genes), the UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA (remaining annotations)

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

• Funding: National Human Genome Research Institute (NHGRI) and the U.S. Department of Agriculture (USDA)
• Sequencing and assembly: BCM-HGSC, Houston, TX, USA
• BAC library: Pieter de Jong and Katzutoyo Osoegawa at Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
• UCSC A. mellifera Genome Browser (apiMel2): Andy Pohl, Angie Hinrichs, Jennifer Jackson, and Donna Karolchik
• UCSC A. mellifera Genome Browser (apiMel1): Angie Hinrichs, Brian Raney, Robert Kuhn, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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:
  • Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler (droAna2)
  • TIGR, Rockville, MD, USA, using an assembler produced by Celera (droAna1)
• 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

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.

• 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

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.

• 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

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.

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:
  • Euchromatic sequence - BDGP, Berkeley, CA, USA
  • Heterochromatic sequence - Drosophila Heterochromatin Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
• Annotations:
  • Euchromatic regions - FlyBase
  • Heterochromatic regions - DHGP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
• UCSC D. melanogaster Genome Browser and additional annotations (dm6): Hiram Clawson, Angie Hinrichs, and Matthew Speir
• UCSC D. melanogaster Genome Browser and additional annotations (dm3): Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
• UCSC D. melanogaster Genome Browser and additional annotations (dm2): Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
• UCSC D. melanogaster Genome Browser and additional annotations (dm1): Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA

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

• Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler
• Funding: National Human Genome Research Institute (NHGRI), USA
• UCSC D. mojavensis Genome Browser (droMoj2): Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik
• UCSC D. mojavensis Genome Browser (droMoj1): Angie Hinrichs, Brian Raney, Galt Barber and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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.

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.

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

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.

These data were provided with the following acknowledgments:

• Sequencing and assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
• UCSC D. simulans Genome Browser (droSim1): Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing, assembly and AGP creation: The Genome Institute at Washington University (WUSTL)
• Initial Sequencing Proposal, Project Collaboration: David J. Begun and Charles H. Langley, University of California, Davis, CA, USA
• UCSC D. yakuba Genome Browser (droYak2): Angie Hinrichs, Jennifer Jackson and Donna Karolchik
• UCSC D. yakuba Genome Browser (droYak1): Angie Hinrichs, Michael Chalup and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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.

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.

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.

UCSC Sacchromyces cerevisiae Genome Browser (sacCer3): Hiram Clawson, Greg Roe, Steve Heitner.
The April 2011 Sacchromyces cerevisiae genome assembly is based on sequence dated April 2011 in the Sacchromyces Genome Database (SGD). This genome sequence was downloaded from NCBI (genbank/genomes/Eukaryotes/fungi/Saccharomy ces_cerevisiae/SacCer_Apr2011/). The SGD™ gene annotations were downloaded from the SGD downloads site. The S288C strain was used in this sequencing project.

The June 2008 Sacchromyces cerevisiae genome assembly (sacCer2) is based on sequence dated June 2008 in the Sacchromyces Genome Database (SGD) and was obtained from the site http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/ The S288C strain was used in this sequencing project.

The Oct. 2003 Sacchromyces cerevisiae genome assembly (sacCer1) is based on sequence dated 1 Oct. 2003 in the Sacchromyces Genome Database (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site http://www.yeastgenome.org/download-data/sequence. The cellular localization and protein abundance data displayed in the Gene Sorter are taken from the Yeast GFP Fusion Localization Database.

See the SGD Systematic Sequencing Table for credit and contact information for each of the chromosomes in the assembly. We'd like to thank Stanford University, the SGD, the University of California San Francisco (UCSF), Washington University in St. Louis, and The Broad Institute for providing the data and annotations for this release.

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

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.

The Ebola virus genome assembly has the following acknowledgments:

• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
• UCSC Ebola virus (eboVir3) Genome Browser: Hiram Clawson, Brian Raney, Maximillian Haeussler, Angie Hirichs, Kate Rosenbloom, Chris Eisenhart, Pauline Fujita, Matthew Speir, Donna Karolchik, Ann Zweig, David Haussler, and Jim Kent
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

Thank you to Phillip Berman and his lab at UCSC for providing continued feedback on the Ebola virus Genome Browser, and to the Pardis Sabeti Lab at the Broad Institute for their guidance.

Thank you to the following institutions for proving additional annotations on the Ebola virus genome:

• National Center for Biotechnology Information (NCBI)
• Immune Epitope Database (IEDB)
• UniProt
• RCSB Protein Data Bank (PDB)

• Affymetrix: Consensus and exemplar sequences for probe selection on several chips, exon array data, transcriptome data, Genie Gene predictions, design and analysis support in the early stages of the UCSC Human Genome project, including software for the synthetic chromosome 22 data we used to test our assembly methods.
• Agilent Technologies (Shane Giles, Peter Webb, and Dione Bailey): Agilent microarray probe sets.
• Allen Institute for Brain Science: Allen Brain Atlas probes.
• BAC Resource Consortium: Cytogenetic markers (FISH-mapped clones annotation track).
• Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) (Richard Gibbs, John Bouck, Kim Worley and James Durbin): Rat Genome sequence data, D. pseudoobscura sequence for alignment tracks with D. melanogaster genome.
• Berkeley Drosophila Genome Project (BDGP): Data for D. melanogaster gene annotations.
• BioBase: Transfac database data used in HMR Conserved Transcription Factor Binding Sites track.
• Bioinformatics Solutions, Inc. (Ming Li and colleagues): Pattern Hunter mouse homology track.
• Biomarkers Consortium: I-SPY collaboration on the UCSC Cancer Genome Browser project.
• Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST): H-InvDB Gene Predictions.
• Boston University (Tullius Lab, in collaboration with MIT, NHGRI, and the La Jolla Institute for Allergy and Immunology): ORChID Predicted DNA Cleavage Sites (ENCODE).
• The Broad Institute
  --(Eric Lander, Mike Zody, Chad Nusbaum): Plasmid end reads. Human working draft sequence analysis project. Special thanks to Eric for inviting us to join the Hardcore Analysis Group for the draft sequence project and for his direction of that group.
  --(Bernstein Lab): Histone modifications using ChIP-seq (ENCODE).
• California Institute of Technology (Wold Lab): RNA-Seq data (ENCODE).
• Canada's Michael Smith Genome Sciences Centre: ORegAnno data, brain DNA methylation track (ENCODE).
• Cedars-Sinai Medical Center (CSMC): FISH-mapped clones annotation track.
• Centre for Applied Genomics: Database of Genomic Variants (DGV) data.
• Centre d'Etude du Polymorphisme Humain (CEPH): Data from Genotype database for SNP Population Allele Frequencies track.
• Centre for Genomic Regulation (CRG) (Guigo Lab): CRG mappability (alignability) data, RNA-seq data.
• CNRS Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France (Michel Weber): miRNA Data annotation track (in collaboration with Sam Griffiths-Jones of The Wellcome Trust Sanger Institute).
• Cold Spring Harbor Laboratory (CSHL)
  --(Stein Lab): HapMap data.
  --(Gingeras Lab and Hannon Lab): RNA-seq data tracks (ENCODE).
  --(Ivo Grosse and Michael Q. Zhang): Predictions for First Exon Finder annotation track.
• Consensus Coding Sequence Project (EBI, NCBI, WTSI, UCSC): Consensus CDS Genes.
• Cornell University (Siepel Lab): Exoniphy.
• Duke University (Institute for Genome Sciences and Policy): Open chromatin track, Human tissue Affymetrix Exon expression array data (ENCODE).
• EMBL (Peter Bork): Mouse pseudogene predictions used for Bork Pseudogenes custom annotation track.
• Emory University School of Medicine (D. Ledbetter, C. Martin): Collaboration on CGH-ICSA grant.
• Ensembl (Paul Flicek, Guy Slater, Imre Vastrik, Arek Kasprzyk, Michele Clamp): Ensembl Gene predictions, data exchange formats, TPF clone map coordination, exonerate mouse homology track, early help placing FISH-mapped clones.
• European Institute of Oncology: Nuclease accessible sites (ENCODE).
• FlyBase: Curated Drosophila gene annotations.
• Fred Hutchison Cancer Research Center (FHCRC) (Barbara Trask): FISH-mapped clones annotation track.
• Gene Ontology (GO) Consortium: Structured annotations for Gene Sorter.
• Genetic Information Research Institute (GIRI): Repbase repeat library, repeatmasking tools.
• Genome Informatics Research Lab (GIRL) within Grup de Recerca en Informàtica Mèdica (GRIB) (Francisco Câmara Ferreira, Roderic Guigó): Geneid and SGP gene prediction annotation tracks.
• Genomics Institute of the Novartis Research Foundation (GNF): Expression data using Affymetrix chips for GNF Expression Atlas annotation tracks.
• Genome Institute of Singapore (GIS): DNA Paired-end Ditag data, RNA-seq data (ENCODE).
• Genoscope (Jean Weissenbach and Olivier Jaillon): Exofish program, Tetraodon nigroviridis sequence for Tetraodon Blat alignments annotation tracks, data for Anopheles Evolutionary Conserved Regions annotation track.
• Helicos BioSciences: RNA-seq data (ENCODE).
• Hospital for Sick Children (Sick Kids) (L. Feuk): Structural variation data.
• HudsonAlpha Institute for Biotechnology (Myers Lab): RNA-seq data (ENCODE), Methyl-seq data (ENCODE), transcription factor binding sites identified by ChIP-seq (ENCODE), copy number variation (CNV) data (ENCODE).
• Illumnia: Probe set alignments.
• Institute for Genomic Research (TIGR): TIGR Gene Index annotation track.
• Institute for Systems Biology (Arian Smit): RepeatMasker repeat identification and masking software and libraries.
• International Knockout Mouse Consortium: Data for IKMC tracks.
• Iowa State University (J. Murray): Collaboration on FaceBase project.
• J. Craig Venter Institute: Nuclease accessible sites (ENCODE).
• Jackson Laboratory: Mouse Genome Informatics tracks, Mouse ortholog links from known genes track.
• Kyoto University, GenomeNet: Kyoto Encyclopedia of Genes and Genomes (KEGG) - pathway diagrams for Known Genes annotation track.
• Lawrence Berkeley National Laboratory (L.A. Pennacchio): Vista HMR-Conserved non-coding human enhancers track.
• Los Alamos National Laboratory (LANL): FISH-mapped clones annotation track.
• Massachusetts Institute of Technology (MIT) (Chris Burge): RNA-Seq data, Genscan gene prediction program.
• Medical College of Wisconsin: Rat Genome Database (RGD).
• Medical Research Council Laboratory of Molecular Biology: Superfamily database.
• Mount Sinai School of Medicine (Gary Benson - now at Boston University): Tandem Repeats Finder.
• National Cancer Institute (NCI), NIH:
  --The Cancer Genome Atlas (TCGA).
  --Mammalian Gene Collection (MGC) Project.
  --Cancer Genome Anatomy Project (CGAP).
  --SAGE project (in collaboration with NCBI).
  --FISH-mapped clones annotation track.
• National Center for Biotechnology Information (NCBI), NIH
  --RefSeq, Entrez Gene, dbSNP, HapMap, OMIM, and PubMed databases.
  --Serial Analysis of Gene Expression Tag to Gene Mapping (SAGEmap) data resource.
  --(Deanna Church): Mouse synteny track, database of whole genome shotgun mouse reads and assemblies used for mouse tracks.
  --(Greg Schuler): GenBank freezes of human clones used in the assembly, NT contigs of multiple finished clones, STS maps (in earlier freezes), specially-formatted versions of the finished chromosomes.
  --(Steve Sherry): SNP tracks.
  --(Wonhee Jang): FISH-mapped clones annotation track.
  --(Danielle and Jean Thierry-Mieg): Acembly Genes annotation track.
  --(Lukas Wagner): 3' EST track in the July 2000 browser.
• National Human Genome Research Institute (NHGRI), NIH
  --(Elnitski Lab): Bidirectional promoters, negative regulatory elements (ENCODE).
  --(ENCODE group): Guidance for ENCODE DCC, collaboration and contributions for various ENCODE annotation tracks.
  --GWAS: GWAS data from the Catalog of Published Genome-Wide Association Studies.
  --(NISC group): Collaboration and annotations for NISC browser, including curated gene annotations, DNAse I Hypersensitive Sites annotation, Multi-species Conserved Sequences (MCS) tracks, Binomial_25 Conservation Scores, ZooSeq Blastz alignments tracks.
• National Institute on Aging, NIH: Data from the Genetic Association Database.
• Netherlands Cancer Institute (van Steensel Lab): Nuclear lamina associated domains tracks.
• Ohio State University Bioinformatics & Computational Biology Group (Ramana V. Davuluri): Predictions for First Exon Finder annotation track.
• ORFeome Collaboration: ORFeome Collaboration human gene clones.
• Pennsylvania State University Center for Comparative Genomics and Bioinformatics: BLASTZ, LASTZ, and multiz alignment programs, Genome Alignment and Annotation Database (GALA), collaboration on multiple alignment annotation tracks, ENCODE annotation tracks, Personal Genome Variants track, Galaxy, regulatory potential scores tracks.
• Perlegen Sciences: STS markers for the Haplotype Blocks annotation track on chr 21, SNP data for the Affymetrix 120K SNP track, TNG radiation hybrid map.
• RIKEN Genomic Sciences Center: Chimpanzee BAC end sequence data, mouse annotations, human genome sequence contributions, CAGE tags RNA subcellular localization data (ENCODE).
• Roswell Park Cancer Institute (RPCI): FISH-mapped clones annotation track.
• SNP Consortium: Data for SNP annotation tracks.
• Softberry Inc. (V. Solovyev): Fgenesh++ and Fgenesv+ gene predictions, TSSW promoters tracks.
• Sperling Biomedical Foundation (Thomas Pringle): Technical consultant on Proteome Browser, avid Genome Browser user and the source of myriad ideas for expanding its functionality, early assistance and support for UCSC Genome Browser.
• Stanford University
  --(Bejerano Lab): GREAT tool.
  --( Morrison Institute for Population and Resource Studies, Human Genome Diversity Project): Data for SNP Population Allele Frequencies track.
  --SOURCE tool: SOURCE links from UCSC Genes tracks.
• Stanford University School of Medicine (Myers Lab - now at HudsonAlpha): Data set for Human Promoters custom annotation track.
• SwitchGear Genomics (N. Trinklein and S.F. Aldred): Transcription start sites (TSSs).
• UniProt: Protein data from UniProt database.
• Universidad de Granada, Grupo de Bioinformática, Spain (Jose L. Oliver): Isochore custom annotation track.
• University at Albany - SUNY (TenenBaum Lab): Target RNA binding protein expression measured by RIP-chip (ENCODE).
• University of CA, Berkeley (Lior Pachter, Simon Cawley, Marina Alexandersson): SLAM Gene predictions.
• University of CA, San Diego
  --(G. Yeo, now at Salk Institute): FOX2 adaptor-trimmed CLIP-seq reads track.
  --(Ren Lab, Ludwig Institute for Cancer Research): TAF1 binding in fibroblastoid cells assayed by ChIP-chip (ENCODE).
• University of CA, San Francisco: Collaboration on UCSC Cancer Browser, Chimera links from SNPs and UCSC Genes, FISH-mapped clones annotation track.
  --(ENCODE group): Brain DNA methylation track (ENCODE).
• University of CA, Santa Cruz
  --(R.E. Green): Neanderthal annotation tracks.
  --(Lowe Lab): tRNA Gene Predictions using tRNAscan-SE.
• University of Cambridge, Department of Oncology: Open chromatin track (ENCODE).
• Stanford University (Pritchard Lab): Collaboration on Human Genome Diversity Project tracks.
• University of North Carolina, Chapel Hill (Lieb Lab, now at the University of Chicago): Open chromatin track (ENCODE).
• University of Pennsylvania (Y. Thomas Gan): Database of Transcribed Sequences (DoTS) Genes custom annotation track.
• University of Pittsburgh (M. Marazita): Collaboration on FaceBase project.
• University of Tennessee GeneNetwork: GeneNetwork links from UCSC Genes annotations.
• University of Texas Health Science Center, Greehy Children's Cancer Research Institute (L.O.F. Penalva):
• University of Texas, Austin (Iyer Lab): Open chromatin track (ENCODE).
• University of Vienna, Institute for Theoretical Chemistry and Structural Biology, Theoretical Biochemistry Group: Vienna RNA utility RNAplot - Known Genes annotation track.
• University of Washington
  --(Eichler Lab): Segmental duplications data.
  --(Human Genome Structural Variation Project): Variation data for HGSV tracks.
  --(ENCODE group): Digital DNase genomic footprinting track, DNaseI sensitivity using digital DNaseI methodology, DNaseI hypersensitive sites, histone modifications using ChIP-seq (ENCODE).
  --(Noble Lab): Predicted nucleosome occupancy tracks.
  --(Nickerson Lab): Tajima's D SNPs track.
• Uppsala University (Wadelius Lab): ChIP-chip data (ENCODE).
• Washington University in St. Louis and Washington University in St. Louis School of Medicine
  --(Robert Waterston (now at UW), John McPhearson, Asif Chinwalla, Shiaw-Pyng Yang, John Wallis and LaDeana Hillier): Fingerprint-based map of BAC clones from the human genome and a corresponding layout of sequenced clones, plasmid end reads, BACend analysis, CpG islands.
  --(Sean Eddy and Todd Lowe (now at UCSC)): RNA Genes track.
  --(Michael Brent Lab): N-SCAN and Twinscan Genes.
  --(ENCODE group): Brain DNA methylation track (ENCODE).
• Wellcome Trust Sanger Institute
  --(J. Harrow, J. Gilbert, J. Sulston, J. Rogers, J. Mullikin, R. Durbin, S. Searle, I. Dunham and the annotation teams): Vega Genes and Pseudogenes, Sanger 20 and Sanger 22 Genes and Pseudogenes. Plasmid end reads, processing of whole genome shotgun mouse reads. Eponine program.
  --(S. Griffiths-Jones): miRNA Data annotation track (in collaboration with M. Weber of CNRS Université Paul Sabatier).
  --Decipher
  --Protein Families Database of Alignments and HMMs (Pfam).
• Whitehead Institute, Bioinformatics and Research Computing (G. Bell): TargetScan miRNA regulatory sites.
• WormBase (Lincoln Stein): Wormbase curated gene annotations for C. elegans genome.
• Yale University:
  --(Snyder, Gerstein, and Weissman Labs in collaboration with NASA Ames Research Center and Eloret Corporation): Transcriptionally Active Regions (TARs) data (ENCODE).
  --(Sestan Lab): Exon microarray expression data from the late mid-fetal human brain.

During the initial stage of this project, from January 2000 to June 2001, we received no direct federal funding to develop the working draft other than travel support. However, we gratefully acknowledge the support for our personnel provided by our basic bioinformatics research grants, especially DOE grant DE-FG03-99ER62849 (to develop gene-finding methods), but also NSF grant DBI-9809007, UC BIOTECH grant 99-11, a grant from the Sloan Foundation, the David and Lucille Packard Foundation, NIH grant GM-52848, and the Zahler grant that provided support for Jim Kent in the early stages of this work.

We are particularly thankful for the risks that Patrick Mantey (UCSC Dean of Engineering), James Gill (Vice Chancellor for Research), John Simpson (UCSC Provost), and M.R.C. Greenwood (UCSC Chancellor) were willing to take in advancing us the money in February 2000 needed to build the original 100-node LINUX cluster used in this work, and in the case of Dean Mantey, additional personnel support. Phokion Kolaitis, Chair of Computer Science, contributed as well.

We thank Compaq for providing an additional 100-CPU computational cluster in Cambridge, MA for use by the public human genome effort. We thank ILOG, Inc. (now part of IBM) for providing discounted licenses to its CPLEX linear programming software, which was essential for some of our early experiments.

In December 2000, HHMI began providing support for equipment and personnel. In the summer of 2001, HHMI provided the primary funding for a new cluster of 1000 CPUs running LINUX purchased from Rackable (now SGI), with additional support from CISI and NHGRI. Dubbed the UCSC KiloKluster, this equipment became the computational backbone for the initial years of the Genome Browser project.