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.
Acknowledgment of early support
UCSC Genome Browser project team
The UCSC Human Genome Browser is generated by the UCSC Genome Bioinformatics Group in collaboration with the International Human Genome Project. The browser project is funded by grants from the National Human Genome Research Institute, and generous support from the Howard Hughes Medical Institute and the California Institutes for Science and Innovation.
We work with collaborators at many other institutions to produce and annotate this reference sequence of the human genome. To view complete acknowledgments for a specific annotation, see the "Credits" section on the track's description page in the Genome Browser. For a list of browser-related publications, see our publications page.
UCSC Human Genome Browsers:
Recent versions of the human genome sequence, starting with the hg19 (GRCh37) assembly, are provided by the Genome Reference Consortium (GRC), whose goal is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary.
Prior to hg19, the human genome sequence data used by the browser were generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data were generated by NCBI, and EST, mRNA, BACend and other types of data used for the assembly and annotation were obtained from GenBank, European Molecular Biology Lab (EMBL), and DNA Data Bank of Japan (DDBJ). Clone maps were created by the individual sequencing centers.
The original chromosome files were produced by the institutions and individuals listed in the table below.
| Chromosome | 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 |
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Alpaca Genome Browser/Annotations:
The alpaca sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The data are provided with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Armadillo Genome Browser/Annotations:
The armadillo sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The data are provided with the following understanding:
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/Annotations:
The baboon sequence is made freely available for public use by the Baboon Genome Sequencing Consortium. Please review the BCM-HGSC conditions for use guidelines before using this data.
Sequencing/Assembly: University of Maryland, College Park, MD, USA
UCSC Bison Genome Browser/Annotations:
The bison sequence is made freely available by the University of Maryland Genome Assembly Group, Aleksey Zimin.
Funding: Italian grant Futuro in Ricerca 2010-RBFR103CE3 and the Howard Hughes Medical Institute
Sequencing/Assembly:
Eichler Laboratory,
Department of Genome Sciences, University of Washington, Seattle
Mario Ventura
Università degli studi di Bari Aldo Moro
UCSC Bonobo Genome Browser/Annotations:
The bonobo sequence is made freely available by the University of Bari and University of Washington.
Funding: European Research Council (grant 233297, TWOPAN) and the Max Planck Society
Sequencing/Assembly: Max-Planck Institute for Evolutionary Anthropology, Germany
UCSC Bonobo Genome Browser/Annotations:
The bonobo sequence is made freely available by the Max-Planck Institute for Evolutionary Anthropology. The initial analysis of this dataset can be found in Prüfer K et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 2012 Jun 28;486(7404):527-31. PMID: 22722832
Sequencing/Assembly: Max-Planck Institute for Evolutionary Anthropology, Germany
UCSC Brown Kiwi Genome Browser/Annotations:
The brown kiwi sequence is made freely available by the Max-Planck Institute for Evolutionary Anthropology. The initial analysis of this dataset can be found in Le Duc D et al. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol. 2015 Jul 23;16:147. PMID: 26201466
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Bushbaby Genome Browser/Annotations:
The bushbaby sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The data are provided with the following understanding:
Sequencing/Assembly:
UCSC Cat Genome Browser/Annotations (felCat9): Hiram Clawson and Conner Powell
The UCSC felCat8 and felCat5 Genome Browsers display data produced by the International Cat Genome Sequencing Consortium:
Funding: National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
454 Production Sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
BAC sequencing: The Genome Institute at WUSTL
Plasmid and fosmid sequencing: The Broad Institute, Cambridge, MA, USA and Agencourt Bioscience
Sequence assembly and data integration for creation of chromosomal AGP files: The Genome Institute at WUSTL
Cat RH map: Bill Murphy, Texas A&M University, College Station, TX, USA.
DNA source: Dr. Kristina Narfstrom, University of Missouri, Columbia, MO, USA.
UCSC Cat Genome Browser/Annotations:
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.
Sequencing/Assembly:
UCSC Cat Genome Browser/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).
Funding: National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
Project Leadership: The Broad Institute, Cambridge, MA, USA
Sequencing/Assembly: The Broad Institute - team led by by Kerstin Lindblad-Toh
Plasmid and fosmid libraries: The Broad Institute
BAC end sequencing: Agencourt Bioscience, Danvers, MA, USA
UCSC Cat Genome Browser/Annotations (felCat3): Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil
The catChrV17e cat assembly was initially published in Pontius JU et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 2007 Nov;17(11):1675-89. PMID: 17975172; PMCID: PMC2045150
The Broad Institute released the initial 2X (v3) assembly of the cat genome as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The cat sequence is made freely available with the following understanding:
The UCSC Chimpanzee Genome Browsers display whole-genome assembly data produced by the University of Washington:
and draft assembly data produced by the Chimpanzee Genome Sequencing Consortium:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly (panTro6):
The whole-genome assembly of a male chimpanzee, Clint (Yerkes pedigree number C0471) was done in stages, resulting in three progressive versions:
Sequencing/Assembly (panTro5):
Sequencing/Assembly (panTro2, panTro3, panTro4):
Sequencing/Assembly (panTro1): Sequence assembled by teams led by Eric Lander, Ph.D. at The Broad Institute and Richard K. Wilson, Ph.D. at The Genome Institute at WUSTL
Alignments: LaDeana Hillier, The Genome Institute at WUSTL and The Broad Institute
Annotations:
UCSC Chimp Genome Browser:
The initial sequencing and analysis of the chimpanzee genome was published by the Chimpanzee Sequencing and Analysis Consortium. The chimpanzee sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87. PMID: 16136131
Sequencing/Assembly: Eagle Genomics Ltd
UCSC Chinese Hamster Genome Browser/Annotations:
The Chinese hamster sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Lewis NE et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug;31(8):759-65.
Funding: NIH-NHGRI grant 5U54HG00307907 to RKW, Director of The Genome Institute at Washington University
DNA source: Dr. Stephen O'Brien at St. Petersburg State University
Sequencing/Assembly: Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
UCSC Chinese Pangolin Genome Browser/Annotations:
The Chinese pangolin sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged: Dr. Richard K. Wilson and The Genome Institute, Washington University School of Medicine.
The UCSC Cow Genome Browser displays three different assemblies of the bovine genome: one provided by the University of Maryland Center for Bioinformatics and Computational Biology (UMD CBCB), one from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), and a third one from the USDA Agricultural Research Service (USDA ARS). The assemblies available in the browser include:
The UMD CBCB genome assemblies are 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/Annotations:
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/Annotations:
The cow sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite the appropriate publication when using these data.
UMD cow assembly: Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10(4):R42.
Baylor cow assembly: Bovine Genome Sequencing and Analysis Consortium. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8.
For more information see the UMD CBCB and the BCM-HGSC Bovine Genome Project pages.
Funding: National Human Genome Research Institute (NHGRI)
DNA source: Dr. Jay Kaplan, Wake Forest Primate Facility, Wake Forest, NC
Genome Sequence: Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
Sequence Assembly: Richa Agarwala, Sergey Shiryaev, NCBI and The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
Assembly curation: LaDeana Hillier, Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
FISH mapping data: Mariano Rocchi, Department of Biology, University of Bari, Bari, Italy
UCSC Crab-eating Macaque Genome Browser/Initial Annotations:
The crab-eating macaque data are provided with the following understanding:
canFam5 submitter: The University of Michigan.
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/Annotations:
The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite this publication when using these data:
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438(7069):803-19. PMID: 16341006
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/Annotations:
The dolphin sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The dolphin data are provided with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Elephant Genome Browser/Annotations:
The elephant sequence is made freely available before scientific publication with the following understanding:
Funding: National Institute of Allergy and Infectious Diseases (NIAID), Genomic Sequencing Centers for Infectious Diseases (GSCID) program
Sequencing/Assembly: Ferret Genome Sequencing Consortium and The Broad Institute, Cambridge, MA, USA
UCSC Ferret Genome Browser/Annotations:
The ferret sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M et al. The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nat Biotechnol. 2014 Dec;32(12):1250-5.
Sequencing/Assembly: The Genome Institute at Washington University School of Medicine
UCSC Garter Snake Genome Browser/Annotations:
The garter snake sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly:
UCSC Gibbon Genome Browser/Annotations:
The gibbon sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11;513(7517):195-201.
Sequencing/Assembly: The Genome Institute at Washington University School of Medicine
UCSC Golden eagle Genome Browser/Annotations:
The golden eagle sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding:
Sequencing/Assembly: Novogene
UCSC Golden Snub-Nosed Monkey Genome Browser/Annotations:
The golden snub-nosed monkey sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Zhou X, Wang B, Pan Q, Zhang J, Kumar S, Sun X, Liu Z, Pan H, Lin Y, Liu G et al. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. Nat Genet. 2014 Dec;46(12):1303-10. PMID: 25362486
The UCSC gorGor6 Genome Browser displays data from the Aug 2019 assembly of from the University of Washington.
Sequencing/Assembly: University of Washington
UCSC Gorilla Genome Browser/Annotations:
The UCSC gorGor5 Genome Browser displays data from the Mar 2016 assembly of Gorilla gorilla gorilla produced by the University of Washington with the following acknowledgments:
Sequencing/Assembly: University of Washington
UCSC Gorilla Genome Browser/Annotations:
The UCSC gorGor4 and gorGor3 Genome Browsers display data produced by the Wellcome Trust Sanger Institute with the following acknowledgments:
Sequencing/Assembly:
UCSC Gorilla Genome Browser/Annotations:
The gorilla sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012 Mar 7;483(7388):169-75. PMID: 22398555; PMCID: PMC3303130
Additionally, this publication discusses the gorGor5 assembly:
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW et al. Long-read sequence assembly of the gorilla genome. Science. 2016 Apr 1;352(6281):aae0344. PMID: 27034376; PMCID: PMC4920363
The green monkey assembly is provided by the Vervet Genomics Consortium with the following acknowledgments:
Funding: National Human Genome Research Institute (NHGRI)
DNA source: Dr. Jay Kaplan, Wake Forest Primate Facility, Wake Forest, NC, USA
Genome Sequence:
BAC Library: Dr. Pieter DeJong, CHORI, Oakland, CA, USA
Assembly Curation:
FISH Mapping Data: Mariano Rocchi, Department of Biology, University of Bari, Bari, Italy
cDNA data - RNA sources: Dr. Nelson Freimer - Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, CA, USA
UCSC Green Monkey Genome Browser/Annotations:
The green monkey sequence is made freely available before scientific publication with the following understanding:
Funding: National Human Genome Research Institute
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Guinea Pig Genome Browser/Annotations:
The guinea pig sequence is made freely available before scientific publication with the following understanding:
Sequencing/Assembly: Johns Hopkins University, Baltimore, MA, USA
UCSC Hawaiian monk seal Genome Browser/Annotations:
The Hawaiian monk seal sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged: Alan F. Scott at Johns Hopkins University.
Mohr DW, Naguib A, Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe D, Scott AF. Improved de Novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost. BioRxiv. 2017 April 18 (preprint).
Sequencing/Assembly: The Broad Institute at MIT and Harvard, Cambridge, MA, USA
DNA Samples: Dr. Neil J. Gemmell - Reproduction, Genomics and Development Group, University of Otago, Dunedin, New Zealand
UCSC Hedgehog Genome Browser/Annotations:
The hedgehog sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The hedgehog data are provided with the following understanding:
The UCSC equCab3 Genome Browser displays data produced by the University of Louisville:
Sequencing/Assembly: University of Louisville, Louisville, KY, USA
UCSC Horse Genome Browser/Annotations: Hiram Clawson and Conner Powell
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/Annotations:
The horse sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest Jr., Brian P. Walenz, Matthew S. Hestand et al. Improved reference genome for the domestic horse increases assembly contiguity and composition. Nature, Commincations Biology. 2018 Nov 16;197:2399-3642
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009 Nov 6;326(5954):865-7.
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/Annotations:
The kangaroo rat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The kangaroo rat data are provided with the following understanding:
Funding: National Institutes of Health (NIH)
Assembly/Sequencing: The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
DNA Source: William Murphy - VIBS, Texas A&M University, College Station, TX, USA
UCSC Malayan Flying Lemur Genome Browser/ Annotations:
The Malayan flying lemur sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged: Richard K. Wilson and The Genome Institute, Washington University School of Medicine.
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Manatee Genome Browser/Annotations:
The manatee sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Foote AD, Liu Y, Thomas GW, Vinař T, Alföldi, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V et al. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015 Mar;47(3):272-5. PMID: 25621460; PMCID: PMC4644735
The UCSC calJac4 Genome Browser displays data from the May 2020 assembly of white-tufted-ear marmoset produced by the McDonnell Genome Institute at Washington University with the following acknowledgments:
Sequencing and assembly: McDonnell Genome Institute at Washington University
DNA Source: Wisconsin Primate Research Center
UCSC Marmoset Genome Browser/Annotations:
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/Annotations:
These data were produced by The Genome Institute at WUSTL and the BCM-HGSC and can be downloaded here.
The marmoset sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:
Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014 Aug;46(8):850-7. PMID: 25038751; PMCID: PMC4138798
Additionally, this publication discusses the calJac4 assembly:
Wang W, Liu JY, Wang HF, Yang MY, Liu QY, Ding MX. The complete mitochondrial genome of white-tufted-ear marmoset, Callithrix jacchus (Primates: Callitrichinae). Mitochondrial DNA A DNA Mapp Seq Anal. 2016 May;27(3):1920-1. PMID: 25329280 doi: 10.3109/19401736.2014.971287
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly:
UCSC Megabat Genome Browser/Annotations:
The megabat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The megabat data are provided with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Little brown bat Genome Browser/Annotations:
The Little brown bat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The Little brown bat data are provided with the following understanding:
Sequencing/Assembly: Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
UCSC Minke Whale Genome Browser/Annotations:
The minke whale genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 2014 Jan;46(1):88-92. PMID: 24270359
Starting with mm10 (GRCm38), the mouse genome assembly is now provided by the Genome Reference Consortium (GRC). See the GRC Mouse Genome web pages for acknowledgments.
UCSC Mouse Genome Browser (mm10): Hiram Clawson and Luvina Guruvadoo
UCSC Mouse Genome Browser (mm39): Hiram Clawson and Jairo Navarro
Prior to mm10/GRCm38, mouse assemblies were produced by the Mouse Genome Sequencing Consortium, with these acknowledgments:
Funding:
Sequencing:
Physical Map:
Assembly: Deanna Church, Richa Agarwala, Josh Cherry, Mike DiCuccio, Hsiu-Chuan Chen, Paul Kitts, Victor Sapojnikov
cDNA Sequencing:
UCSC Mouse Genome Browser:
Annotations:
The initial 3X coverage of the mouse genome was produced by the Mouse Sequencing Consortium, with the following acknowledgments:
Project Oversight: Arthur Holden and Francis Collins
Funding:
Sequencing:
The mouse genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. PMID: 12466850
For more information about mouse assemblies provided by the GRC, see the GRC mouse genome web pages. For information about assemblies prior to mm10/GRCm38, see the Wellcome Trust Sanger Institute Mouse Resource Portal.
Sequep/Assembly:
UCSC Mouse Lemur Genome Browser/Annotations:
The mouse lemur sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The mouse lemur data are provided with the following understanding:
Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China
UCSC Naked Mole-rat Genome Browser/Annotations:
The naked mole-rat genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM et al. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics. 2014 Dec 15;30(24):3558-60.
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
FISH Mapping: North Carolina State University (NCSU), Raleigh, NC, USA
UCSC Opossum Genome Browser/Annotations:
The opossum genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10;447(7141):167-77.
Sequencing:
Sequence Assembly and Chromosomal Sequence/AGP Construction: The Genome Institute at WUSTL
DNA Source:
BAC Library: Yuko Yoshonaga in Pieter de Jong's laboratory, Children's Hospital Oakland Research Institute, Oakland, CA, USA
Fosmid Library: The Genome Institute at WUSTL
Fingerprint Map: The Genome Institute at WUSTL
Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses: Mariano Rocchi, Department of Genetics and Microbiology, University of Bari, Bari, Italy
Fosmid End Placement against the Human Genome (used for breakpoint/inversion analyses during AGP construction): Lin Chen and Evan Eichler, Department of Genome Sciences, University of Washington, Seattle, WA, USA
Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH)
UCSC Orangutan Genome Browser/Annotations:
The orangutan genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-33.
Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE, et al. High-resolution comparative analysis of great ape genomes. Science 2018 Jun 8;360(6393).
Sequencing/Assembly: The Beijing Genomics Institute at Shenzhen
UCSC Panda Genome Browser/Annotations:
The panda genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21;463(7279):311-7. PMID: 20010809
Sequencing/Assembly:
UCSC Pig Genome Browser/Annotations:
The pig genome sequence has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement.
The International Swine Genome Sequencing Consortium genome-wide analyses of the pig genome is described in: Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund LA, Schook LB. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence. BMC Genomics. 2012 Nov 15;13:581. PMID: 23150988
The initial marker paper: Archibald AL, Bolund L, Churcher C, Fredholm M, Groenen MA, Harlizius B, Lee KT, Milan D, Rogers J, Rothschild MF et al. Pig genome sequence--analysis and publication strategy. BMC Genomics. 2010 Jul 19;11:438. PMID: 20642822; PMCID: PMC3017778
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Pika Genome Browser/Annotations:
The pika sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The pika data are provided with the following understanding:
Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
UCSC Platypus Genome Browser/Annotations:
The platypus genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. PMID: 18464734
Sequencing/Assembly: Proboscis Monkey Functional Genome Consortium
UCSC Proboscis Monkey Genome Browser/Annotations:
The proboscis monkey sequence is made freely available before scientific publication with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Rabbit Genome Browser/Annotations:
The rabbit sequence is made freely available before scientific publication with the following understanding:
Sequencing/Assembly: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
UCSC Rat Genome Browser/Annotations:
The rat genome assembly (Rattus norvegicus) is provided by the Rat Genome Sequencing Consortium with the following acknowledgments:
Project Coordination: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)
Funding:
Sequencing:
Assembly: BCM-HGSC ATLAS group - Rui Chen, James Durbin, Paul Havlak
Fingerprint Mapping: The British Columbia Cancer Agency Genome Sciences Center - Marco Marra, Jackie Schein
BAC End Sequencing: The Institute for Genomic Research - Shaying Zhao
BAC Library Construction and Distribution: Children's Hospital Oakland Research Institute (CHORI) - Pieter deJong
Rat Genome Database: Medical College of Wisconsin
UCSC Rat Genome Browser/Annotations:
The rat genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res. 2004 Apr;14(4):721-32. PMID: 15060016
Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521. PMID: 15057822
See the Baylor conditions of use web page for restrictions on the use of these data.
The UCSC Genome Browser displays multiple assemblies of the Rhesus macaque genome produced by different institutions:
The Genome Institute at Washington University School of Medicine assembly is provided with the following acknowledgments:
Macaca mulatta Sequence and Assembly Credits: Sequencing Funds - This work was supported by the NHGRI grant No. 5U24HG00908103, HIGH QUALITY HUMAN AND NON-HUMAN PRIMATE GENOME ASSEMBLIES, at the McDonnell Genome Institute, Washington University School of Medicine DNA source - Coriell sample id: AG07107, MMU Genome Sequencing - The McDonnell Genome Institute, Washington University School of Medicine. Sequence Assembly - The McDonnell Genome Institute, Washington University School of Medicine. Sequence assembly curation - The McDonnell Genome Institute, Washington University School of Medicine; The University of Washington, Seattle, WA.
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:
BAC resources: Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
BAC-based fingerprint map: Genome Sciences Centre, Vancouver, B.C.
For more information on the MMGSC rhesus macaque genome project, see the BCM HGSC Rhesus Monkey Genome Project web page.
UCSC Rhesus Genome Browser/Annotations:
The Macaca mulatta Mmul_9.0 and Mmul_10 assembly sequences are made available to the community by the McDonnell Genome Institute, Washington University, St Louis, MO with the following understanding: Users are free to analyze these data if the providers of this data are properly cited, any whole genome analyses should follow guidelines outlined in the Toronto agreement on the use of this assembly.
The initial sequencing and analysis of the rhesus macaque genome produced by the MMGSC was published in: Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science. 2007 Apr 13;316(5822):222-34. PMID: 17431167
The initial sequencing and analysis of the rhesus macaque genome produced by BGI was published in: Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ et al Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol. 2011 Oct 16;29(11):1019-23. PMID: 22002653
The rhesus macaque sequence is made freely available for public use with the following understanding:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly:
UCSC Rock Hyrax Genome Browser/Annotations:
The rock hyrax sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The rock hyrax data are provided with the following understanding:
Sequencing/Assembly: International Sheep Genomics Consortium (ISGC)
Mitochondrial Genome Sequencing: Justus-Liebig-University, Germany
UCSC Sheep Genome Browser/Annotations:
The sheep genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 Jun 6;344(6188):1168-73. PMID: 24904168
International Sheep Genomics Consortium. The sheep genome reference sequence: a work in progress. Anim Genet. 2010 Oct;41(5):449-53. PMID: 20809919
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Shrew Genome Browser/Annotations:
The shrew sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The shrew data are provided with the following understanding:
Sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Sloth Genome Browser/Annotations:
The sloth sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The sloth data are provided with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Squirrel Genome Browser/Annotations:
The squirrel sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The squirrel data are provided with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Squirrel Monkey Genome Browser/Annotations:
The squirrel monkey sequence is made freely available before scientific publication with the following understanding:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly:
UCSC Tarsier Genome Browser/Annotations:
The tarsier sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The tarsier data are provided with the following understanding:
Sequencing/Assembly: Wellcome Trust Sanger Institute, Cambridge, UK
UCSC Tasmanian Devil Genome Browser/Annotations:
The Tasmanian devil genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C et al. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell. 2012 Feb 17;148(4):780-91. PMID: 22341448
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Tenrec Genome Browser/Annotations:
The tenrec sequence is made freely available before scientific publication with the following understanding:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Tree Shrew Genome Browser/Annotations:
The tree shrew sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357
The tree shrew data are provided with the following understanding:
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/Annotations:
The wallaby genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011 Aug 29;12(8):R81. PMID: 21854559
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/Annotations:
The southern white rhinoceros sequence is made freely available before scientific publication with the following understanding:
Sequencing/Assembly: International Xenopus Sequencing Consortium
UCSC African clawed frog Genome Browser/Annotations:
The African clawed frog genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 20;538(7625):336-343. PMID: 27762356; PMC: PMC5313049
Sequencing/Assembly: International Crocodilian Genomes Working Group
UCSC American Alligator Genome Browser/Annotations:
The American alligator genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol. 2012 Jan 31;13(1):415. PMID: 22293439
Funding: Research Council of Norway (FUGE)
Sequencing/Assembly: GenoFisk Consortium
UCSC Atlantic Cod Genome Browser/Annotations:
The Atlantic cod genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T et al. Large-scale sequence analyses of Atlantic cod. N Biotechnol. 2009 Jun;25(5):263-71. PMID: 19491044
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 2011 Aug 10;477(7363):207-10. PMID: 21832995
Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
UCSC Budgerigar Genome Browser/Annotations:
The budgerigar sequence is made freely available before scientific publication with the following understanding:
Sequencing: The Genome Reference Consortium
Physical Map: The Genome Institute at WUSTL
Genetic Mapping/Linkage Analysis: The Chicken Mapping Consortium:
cDNA sequences: National Institutes of Health and The University of Manchester BBSRC ChickEST Database
RJF finished clones:
Assembly, Assembly/Map Integration, Golden Path Creation: The Genome Institute at WUSTL
SNPs and cross-referenced gene annotations: The Beijing Genomics Institute (BGI), Beijing, China
UCSC Chicken Genome Browser/Annotations:
The chicken genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404
The BGI gene annotations and SNP data are made available with the following terms of use:
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Coelacanth Genome Browser/Annotations:
The coelacanth genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 18;496(7445):311-6. PMID: 23598338
Sequencing/Assembly: Singapore Institute of Molecular and Cell Biology
UCSC Elephant Shark Genome Browser/Annotations:
The elephant shark genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9. PMID: 24402279
The Fugu genome assembly (Takifugu rubripes) is provided by the Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium, led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).
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/Annotations:
The Fugu genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H, Naruse K, Brenner S et al. Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol. 2011;3:424-42. PMID: 21551351
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly:
UCSC Lamprey Genome Browser/Annotations:
The lamprey genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013 Apr;45(4):415-21, 421e1-2. PMID: 234350859
Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
UCSC Lizard Genome Browser/Annotations:
The lizard genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31;477(7366):587-91. PMID: 21881562
The medaka genome assembly (Oryzias latipes) is provided by Japan's National Institute of Genetics (NIG) and the University of Tokyo. The assembly was constructed using the RAMEN assembler.
NOTE: The UCSC oryLat1 assembly was replaced by oryLat2 in Nov. 2008 to correct a UCSC assembly error with chrUn in which the gap relationships between contigs within their ultracontigs were broken. The oryLat2 assembly is based on the same assembly as oryLat1: the v1.0 assembly from NIG and the University of Tokyo.
Sequencing/Assembly: NIG and University of Tokyo, Japan
UCSC Medaka Genome Browser/Annotations:
The medaka genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y et al. The medaka draft genome and insights into vertebrate genome evolution. Nature. 2007 Jun 7;447(7145):714-9. PMID: 17554307
Sequencing/Assembly: Genome 10K Project and Beijing Genomics Institute (BGI)
UCSC Medium Ground Finch Genome Browser/Annotations:
The medium ground finch genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C5, Storz JF, Antunes A, Greenwold MJ, Meredith RW et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20. PMID: 25504712; PMCID: PMC4390078
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Nile Tilapia Genome Browser/Annotations:
The Nile tilapia genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E et al. The genomic substrate for adaptive radiation in African cichlid fish. Nature. 2014 Sep 18;513(7518):375-81. PMID: 25186727; PMCID: PMC4353498
Sequencing/Assembly: International Painted Turtle Genome Sequencing Consortium
UCSC Painted Turtle Genome Browser/Annotations:
The painted turtle genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV et al. Physical mapping and refinement of the painted turtle genome (Chrysemys picta) inform amniote genome evolution and challenge turtle-bird chromosomal conservation. Genome Biol Evol. 2015 Jun 24;7(7):2038-50. PMID: 26108489; PMCID: PMC4524486
Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
UCSC Stickleback Genome Browser/Annotations:
The stickleback sequence is made freely available before scientific publication with the following understanding:
Sequencing/Assembly:
Project Funding:
Initial Genome Browser Annotations:
UCSC Tetraodon Genome Browser:
The Tetraodon genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Yue GH, Lo LC, Zhu ZY, Lin G, Feng F. The complete nucleotide sequence of the mitochondrial genome of Tetraodon nigroviridis. DNA Seq. 2006 Apr;17(2):115-21. PMID: 17076253
Sequencing/Assembly: The Beijing Genomics Institute, Shenzhen, China
UCSC Tibetan Frog Genome Browser/Annotations:
The Tibetan frog genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, Zhong L, Wang L, Wu DD, Zhang BL et al. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1257-62. PMID: 25733869; PMCID: PMC4371989
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/Annotations:
The turkey genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010 Sep 7;8(9). PMID: 20838655
Sequencing/Assembly: University of California, Berkeley, Berkeley, CA, USA
UCSC X. tropicalis Genome Browser/Annotations:
Sequencing/Assembly: Joint Genome Institute (JGI), Walnut Creek, CA, USA
UCSC X. tropicalis Genome Browser/Annotations:
The X. tropicalis genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L et al. The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30;328(5978):633-6. PMID: 20431018
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/Annotation:
The zebra finch genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S et al. The genome of a songbird. Nature. 2010 Apr 1;464(7289):757-62. PMID: 20360741
Starting with the danRer10 (GRCz10) assembly, the zebrafish genome sequence is now provided by the Genome Reference Consortium (GRC). See the GRC Zebrafish Genome web page for acknowledgments.
Most Recent UCSC Zebrafish Genome Browser (danRer11): Christopher Eisenhart, Hiram Clawson, Christopher Lee
Prior assemblies have the following acknowledgments:
Sequencing/Assembly: The Wellcome Trust Sanger Institute, UK.
FPC map:
BAC Clones, BAC End Pairs:
Annotations:
UCSC Zebrafish Genome Browsers:
The zebrafish genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 25;496(7446):498-503. PMID: 23594743
For more information about zebrafish assemblies provided by the GRC, see the GRC zebrafish web pages. For information about assemblies prior to danRer10/GRCz10, see the Sanger Institute's Zebrafish Sequencing Project web page.
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:
Annotations:
UCSC C. intestinalis Genome Browsers:
The C. intestinalis sequence data have been freely provided by the JGI and may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002 Dec 13;298(5601):2157-67. PMID: 12481130
For more information about the C. intestinalis assembly, see the JGI C. intestinalis portal.
Funding: U.S. Department of Energy Office of Science, Biological and Environmental Research Program
Sequencing/Assembly: JGI
UCSC Lancelet Genome Browser/Annotations:
The lancelet genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008 Jun 19;453(7198):1064-71. PMID: 18563158
Funding: National Human Genome Research Institute (NHGRI)
Sequencing/Assembly: BCM-HGSC, Houston, TX, USA
UCSC S. purpuratus Genome Browsers/Annotations:
The sea urchin genome data may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite this publication when using these data:
Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 Nov 10;314(5801):941-52. PMID: 17095691
For more information on the sea urchin genome project, see the BCM-HGSC Sea Urchin Genome Project web page.
The MOZ2 Anopheles gambiae data were provided by the International Anopheles Genome Project and downloaded from Ensembl. The data have the following acknowledgments:
Funding:
Celera Genomics and Genoscope were funded respectively by National Institutes of Health (NIH) and the French Ministry of Research.
Project collaboration: The International Anopheles Genome Project - a collaboration between:
Sequencing and Assembly:
Data Downloads: Ensembl
UCSC A. gambaie Genome Browser/Annotations:
Additional Genome Browser Annotations:
The A. gambaie sequence is made freely available by the International Anopheles Genome Project. Please cite the following publication when using these data:
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002 Oct 4;298(5591):129-49. PMID: 12364791
Funding:
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/Annotations:
The A. mellifera sequence is made freely available by the Honeybee Genome Sequencing Consortium. Please cite the following publication when using these data:
Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006 Oct 26;443(7114):931-49. PMID: 17073008
See the Baylor conditions of use statement for guidelines regarding the use of these data.
The droAna2 data were provided by Agencourt Bioscience. The droAna1 data were produced by the Institute for Genomic Research (TIGR).
Sequencing: Agencourt Bioscience, Danvers, MA, USA
Assembly:
UCSC A. mellifera Genome Browser/Annotations:
The D. ananassae sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler
UCSC D. erecta Genome Browser/Annotations:
The D. erecta sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler
UCSC D. grimshawi Genome Browser/Annotations:
The D. grimshawi sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
The D. melanogaster assemblies displayed in the UCSC Genome Browser were obtained from the Berkeley Drosophila Genome Project (BDGP) with the following acknowledgments:
Sequencing and Assembly:
Annotations:
UCSC D. melanogaster Genome Browser:
For additional information about these data, including citation guidelines, see the BDGP web site.
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/Annotations:
The D. mojavensis sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite these publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC D. persimilis Genome Browser/Annotations:
The D. persimilis sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
Sequencing and Assembly: BCM-HGSC, Houston, TX, USA
UCSC D. pseudoobscura Genome Browser/Annotations:
The D. pseudoobscura data are made available with specific conditions for use. Please cite the following publications:
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 Jan;15(1):1-18. PMID: 15632085; PMCID: PMC540289
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Sequencing/Assembly: The Broad Institute, Cambridge, MA USA
UCSC D. sechellia Genome Browser/Annotations:
The D. sechellia sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
Sequencing and assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA
UCSC D. simulans Genome Browser/Annotations:
The D. simulans sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
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/Annotations:
The D. virilis sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
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/Annotations:
The D. yakuba sequence may be freely downloaded, used in analyses, and repackaged in databases if the data provider is properly acknowledged. Please cite the following publications when using these data:
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-18. PMID: 17994087
Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008 Jan 1;24(1):42-5. PMID: 18057021
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.
The worm sequences are made freely available with the following understanding:
The April 2011 Sacchromyces cerevisiae genome assembly (sacCer3) 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 SGD sequence dated June 2008, 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 SGD sequence dated 1 Oct. 2003. 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 UCSC Gene Sorter are taken from the Yeast GFP Fusion Localization Database.
UCSC Sacchromyces cerevisiae Genome Browser/Annotations:
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 these browsers.
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC California Sea Hare Genome Browser/Annotations:
The California sea hare sequence is made freely available with the following understanding:
Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
UCSC Ebola virus Genome Browser/Annotations:
Other Acknowledgements: Thanks to Phillip Berman and his lab at UCSC for providing continued feedback on the Ebola virus Genome Browser, and to the Pardis Sabeti Lab at the Broad Institute for their guidance.
Thank you to the following institutions for proving additional annotations on the Ebola virus genome:
The Ebola virus sequence may be freely downloaded, used in analyses, and repackaged in databases. The data may be freely used in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged.
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.