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UCSC Genome Browser Acknowledgments

The data and software displayed on this site are the result of a large collaborative effort among many individuals at UCSC and at research institutions around the world. We'd like to acknowledge the scientists and engineers who have contributed to the UCSC Genome Browser and its data, and the organizations who have made this project possible through their generous funding.

Human

Acknowledgment of early support

UCSC Genome Browser project team

Human Genome Browser acknowledgments

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:

Human genome data sources

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

Alpaca genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Alpaca Genome Browser/Annotations:

Data use

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:

Armadillo genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Armadillo Genome Browser/Annotations:

Data use

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:

Baboon genome

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:

Data use

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.

Bison genome

Sequencing/Assembly: University of Maryland, College Park, MD, USA

UCSC Bison Genome Browser/Annotations:

Data use

The bison sequence is made freely available by the University of Maryland Genome Assembly Group, Aleksey Zimin.

Bonobo genome

Funding: European Research Council (grant 233297, TWOPAN) and the Max Planck Society

Sequencing/Assembly: Max-Planck Institute for Evolutionary Anthropology, Germany

UCSC Baboon Genome Browser/Annotations:

Data use

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

Brown kiwi genome

Sequencing/Assembly: Max-Planck Institute for Evolutionary Anthropology, Germany

UCSC Brown Kiwi Genome Browser/Annotations:

Data use

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

Bushbaby genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Bushbaby Genome Browser/Annotations:

Data use

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:

Cat genome

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

Data use

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:

Chimpanzee genome

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

Funding: National Human Genome Research Institute (NHGRI)

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:

Data use

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

Chinese hamster genome

Sequencing/Assembly: Beijing Genomics Institution-Shenzhen

UCSC Chinese Hamster Genome Browser/Annotations:

Data use

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.

Chinese pangolin genome

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:

Data use

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.

Cow genome

The UCSC Cow Genome Browser displays two different assemblies of the bovine genome: one provided by the University of Maryland Center for Bioinformatics and Computational Biology (UMD CBCB) and one from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). The assemblies available in the browser include:

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:

Data use

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.

Crab-eating macaque genome

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:

Data use

The crab-eating macaque data are provided with the following understanding:

Dog genome

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:

Data use

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

Dolphin genome

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:

Data use

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:

Elephant genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Elephant Genome Browser/Annotations:

Data use

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

Ferret genome

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:

Data use

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.

Gibbon genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly:

UCSC Gibbon Genome Browser/Annotations:

Data use

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.

Golden eagle genome

Sequencing/Assembly: The Genome Institute at Washington University School of Medicine

UCSC Golden eagle Genome Browser/Annotations:

Data use

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:

Golden snub-nosed monkey genome

Sequencing/Assembly: Novogene

UCSC Golden Snub-Nosed Monkey Genome Browser/Annotations:

Data use

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

Gorilla genome

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:

Data use

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

Green monkey genome

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:

Data use

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

Guinea pig genome

Funding: National Human Genome Research Institute

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Guinea Pig Genome Browser/Annotations:

Data use

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

Hedgehog genome

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:

Data use

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:

Horse genome

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:

Data use

The horse sequence data may be freely downloaded, used in analyses, and repackaged in databases if the provider is properly acknowledged. Please cite this publication when using these data:

Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009 Nov 6;326(5954):865-7.

Kangaroo rat genome

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:

Data use

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:

Malayan flying lemur genome

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:

Data use

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.

Manatee genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Manatee Genome Browser/Annotations:

Data use

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

Marmoset genome

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:

Data use

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

Megabat genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly:

UCSC Megabat Genome Browser/Annotations:

Data use

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:

Microbat genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Microbat Genome Browser/Annotations:

Data use

The microbat sequence has been made freely available as part of the Mammalian Genome Project (29 Mammals Project). The initial analysis of this dataset can be found in Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. PMID: 21993624; PMCID: PMC3207357

The microbat data are provided with the following understanding:

Minke whale genome

Sequencing/Assembly: Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea

UCSC Minke Whale Genome Browser/Annotations:

Data use

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

Mouse genome

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

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:

Data use

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.

Mouse lemur genome

Sequep/Assembly:

UCSC Mouse Lemur Genome Browser/Annotations:

Data use

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:

Naked mole-rat genome

Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China

UCSC Naked Mole-rat Genome Browser/Annotations:

Data use

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.

Opossum genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

FISH Mapping: North Carolina State University (NCSU), Raleigh, NC, USA

UCSC Opossum Genome Browser/Annotations:

Data use

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.

Orangutan genome

Sequencing:

Sequence Assembly and Chromosomal Sequence/AGP Construction: The Genome Institute at WUSTL

DNA Source: Dr. Greely Stones, Gladys Porter Zoo, Brownsville, TX, USA

BAC Library: Yuko Yoshonaga in Pieter de Jong's laboratory, Children's Hospital Oakland Research Institute, Oakland, CA, USA

Fosmid Library: The Genome Institute at WUSTL

Fingerprint Map: The Genome Institute at WUSTL

Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses: Mariano Rocchi, Department of Genetics and Microbiology, University of Bari, Bari, Italy

Fosmid End Placement against the Human Genome (used for breakpoint/inversion analyses during AGP construction): Lin Chen and Evan Eichler, Department of Genome Sciences, University of Washington, Seattle, WA, USA

Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH)

UCSC Orangutan Genome Browser/Annotations:

Data use

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.

Panda genome

Sequencing/Assembly: The Beijing Genomics Institute at Shenzhen

UCSC Panda Genome Browser/Annotations:

Data use

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

Pig genome

Sequencing/Assembly:

UCSC Pig Genome Browser/Annotations:

Data use

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

Pika genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Pika Genome Browser/Annotations:

Data use

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:

Platypus genome

Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA

UCSC Platypus Genome Browser/Annotations:

Data use

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

Proboscis monkey genome

Sequencing/Assembly: Proboscis Monkey Functional Genome Consortium

UCSC Proboscis Monkey Genome Browser/Annotations:

Data use

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

Rabbit genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Rabbit Genome Browser/Annotations:

Data use

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

Rat genome

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:

Data use

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.

Rhesus genome

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

The BGI assembly is provided with the following acknowledgments:

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

Sequencing/Assembly: BGI, Shenzhen, China

The MMGSC assembly is provided with the following acknowledgments:

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:

Data use

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:

Rock hyrax genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly:

UCSC Rock Hyrax Genome Browser/Annotations:

Data use

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:

Sheep genome

Sequencing/Assembly: International Sheep Genomics Consortium (ISGC)

Mitochondrial Genome Sequencing: Justus-Liebig-University, Germany

UCSC Sheep Genome Browser/Annotations:

Data use

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

Shrew genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Shrew Genome Browser/Annotations:

Data use

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:

Sloth genome

Sequencing: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA

Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Sloth Genome Browser/Annotations:

Data use

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:

Squirrel genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Squirrel Genome Browser/Annotations:

Data use

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:

Squirrel monkey genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Squirrel Monkey Genome Browser/Annotations:

Data use

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

Tarsier genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly:

UCSC Tarsier Genome Browser/Annotations:

Data use

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:

Tasmanian devil genome

Sequencing/Assembly: Wellcome Trust Sanger Institute, Cambridge, UK

UCSC Tasmanian Devil Genome Browser/Annotations:

Data use

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

Tenrec genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Tenrec Genome Browser/Annotations:

Data use

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

Tree shrew genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Tree Shrew Genome Browser/Annotations:

Data use

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:

Wallaby genome

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:

Data use

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

White rhinoceros genome

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:

Data use

The southern white rhinoceros sequence is made freely available before scientific publication with the following understanding:

American alligator genome

Sequencing/Assembly: International Crocodilian Genomes Working Group

UCSC American Alligator Genome Browser/Annotations:

Data use

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

Atlantic cod genome

Funding: Research Council of Norway (FUGE)

Sequencing/Assembly: GenoFisk Consortium

UCSC Atlantic Cod Genome Browser/Annotations:

Data use

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

Budgerigar genome

Sequencing/Assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA

UCSC Budgerigar Genome Browser/Annotations:

Data use

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

Chicken genome

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:

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:

Data use

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:

Coelacanth genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Coelacanth Genome Browser/Annotations:

Data use

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

Elephant shark genome

Sequencing/Assembly: Singapore Institute of Molecular and Cell Biology

UCSC Elephant Shark Genome Browser/Annotations:

Data use

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

Fugu genome

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:

Data use

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

Lamprey genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly:

UCSC Lamprey Genome Browser/Annotations:

Data use

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

Lizard genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA USA

UCSC Lizard Genome Browser/Annotations:

Data use

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

Medaka genome

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:

Data use

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

Medium ground finch genome

Sequencing/Assembly: Genome 10K Project and Beijing Genomics Institute (BGI)

UCSC Medium Ground Finch Genome Browser/Annotations:

Data use

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

Nile tilapia genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC Nile Tilapia Genome Browser/Annotations:

Data use

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

Painted turtle genome

Sequencing/Assembly: International Painted Turtle Genome Sequencing Consortium

UCSC Painted Turtle Genome Browser/Annotations:

Data use

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

Stickleback genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA USA

UCSC Stickleback Genome Browser/Annotations:

Data use

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

Tetraodon genome

Sequencing/Assembly:

Project Funding:

Initial Genome Browser Annotations:

UCSC Tetraodon Genome Browser:

Data use

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

Tibetan frog genome

Sequencing/Assembly: The Beijing Genomics Institute, Shenzhen, China

UCSC Tibetan Frog Genome Browser/Annotations:

Data use

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

Turkey genome

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:

Data use

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

X. tropicalis genome

Sequencing/Assembly: Joint Genome Institute (JGI), Walnut Creek, CA, USA

UCSC X. tropicalis Genome Browser/Annotations:

Data use

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

Zebra finch genome

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:

Data use

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

Zebrafish genome

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.

UCSC Zebrafish Genome Browser (danRer10): Hiram Clawson, Brian Raney, Steve Heitner

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:

Data use

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.

C. intestinalis genome

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:

Data use

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.

Lancelet genome

Funding: U.S. Department of Energy Office of Science, Biological and Environmental Research Program

Sequencing/Assembly: JGI

UCSC Lancelet Genome Browser/Annotations:

Data use

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

S. purpuratus genome

Funding: National Human Genome Research Institute (NHGRI)

Sequencing/Assembly: BCM-HGSC, Houston, TX, USA

UCSC S. purpuratus Genome Browsers/Annotations:

Data use

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.

A. gambiae genome

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:

Data use

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

A. mellifera genome

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:

Data use

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.

D. ananassae genome

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:

Data use

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

D. erecta genome

Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler

UCSC D. erecta Genome Browser/Annotations:

Data use

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

D. grimshawi genome

Sequencing and Assembly: Agencourt Bioscience, Danvers, MA, USA, using the Arachne assembler

UCSC D. grimshawi Genome Browser/Annotations:

Data use

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

D. melanogaster genome

The D. melanogaster assemblies displayed in the UCSC Genome Browser were obtained from the Berkeley Drosophila Genome Project (BDGP) with the following acknowledgments:

Sequencing and Assembly:

Annotations:

UCSC D. melanogaster Genome Browser:

Data use

For additional information about these data, including citation guidelines, see the BDGP web site.

D. mojavensis genome

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:

Data use

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

D. persimilis genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC D. persimilis Genome Browser/Annotations:

Data use

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

D. pseudoobscura genome

Sequencing and Assembly: BCM-HGSC, Houston, TX, USA

UCSC D. pseudoobscura Genome Browser/Annotations:

Data use

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

D. sechellia genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA USA

UCSC D. sechellia Genome Browser/Annotations:

Data use

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

D. simulans genome

Sequencing and assembly: The Genome Institute at Washington University (WUSTL), St. Louis, MO, USA

UCSC D. simulans Genome Browser/Annotations:

Data use

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

D. virilis genome

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:

Data use

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

D. yakuba genome

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:

Data use

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

C. elegans genome

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

Worm Genomes (other than C. elegans)

The latest versions of the C. brenneri, C. briggsae, C. japonica, C. remanei, and P. pacificus sequences were obtained from the Genome Sequencing Center at The Genome Institute at Washington University (WUSTL). The cb1 browser data were obtained from WormBase.

We'd like to thank WUSTL for providing the sequence data for these assemblies, as well as the Sanger Institute for their collaborative work in sequencing the initial C. briggsae cb1 genome. Thanks also to the WormBase consortium for providing access to the cb1 sequence.

Data use

The worm sequences are made freely available with the following understanding:

Yeast genome

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:

Data use

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.

California sea hare genome

Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA

UCSC California Sea Hare Genome Browser/Annotations:

Data use

The California sea hare sequence is made freely available with the following understanding:

Ebola virus genome

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:

Data use

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.

Acknowledgment of early support

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

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

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

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

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