Gentaur’s Genome Browser

Gentaur DNA sequencing Database lits of species DNA.

What are DNA databases?

  1. Some decade ago Sequencing DNA was done to determine the DNA function of genes that may cause diseases.
  2. In the DNA double helix is made of Adenine (A) always pairs with thymine (T); cytosine (C) always pairs with guanine (G).
  3. The National Human Genome Research Institute (NHGRI) Genome Technology Program and its Advanced DNA Sequencing Technology could eventually reduce the cost of sequencing a human genome of even higher quality than is possible today and for less than  800 GBP
  4. Nanopore-based DNA sequencing involves threading single DNA strands through extremely tiny pores in a membrane.
  5. Comparing the genome sequences of different types of animals and organisms, such as mice, rasts, dogs, chimpanzees or yeast, can also provide insights into the biology of development and gene function

Sequencing Lab
Sequencing Lab
  Gentaur Genome Browser 

Gentaur Genome Browser sequence data:

Mammal genes

Other Vertebrates genes

Deuterostome genes

Insect genes

Nematode genes

Other

Viral genes

 

 


  Human Genome Browser Participants

HHMI

CISI

NHGRI

The UCSC Human Genome Browser is generated by the
UCSC Genome Bioinformatics Group in
collaboration with the International Human Genome Project.
The browser project is funded by grants from the
National Human Genome Research Institute,
and generous support from the
Howard Hughes Medical Institute and the
California Institutes for Science and Innovation.

We work with collaborators at many other institutions
to produce and annotate this reference sequence of the human genome.
To view complete acknowledgments for a specific annotation, see the
“Credits” section on the track’s description page
in the Genome Browser. For a list of browser-related publications,
see our publications page.

UCSC Human Genome Browsers:

  • hg38 (GRCh38):
    Hiram Clawson, Brian Raney, Robert Kuhn, Donna Karolchik, Steve Heitner
  • hg19 (GRCh37): Hiram Clawson, Brooke Rhead,
    Pauline Fujita, Ann Zweig, Katrina Learned, Donna Karolchik and Robert Kuhn
  • hg18:
    Engineering effort led by Fan Hsu; QA effort led by Ann Zweig
  • hg17:
    Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik,
    Kate Rosenbloom, Angie Hinrichs, Rachel Harte, and Jim Kent
  • hg16:
    Terry Furey, Hiram Clawson,
    Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent
  • hg15 (archived): Jim Kent, Terry Furey, Matt Schwartz,
    Heather Trumbower, Angie Hinrichs, Fan Hsu, Donna Karolchik, Jorge Garcia,
    Patrick Gavin, Chuck Sugnet, Yontao Lu, Mark Diekhans, Ryan Weber,
    Robert Baertsch, Krishna Roskin, and many other students in the UCSC
    Genome Bioinformatics group
  • Earlier browsers (archived): UCSC Genome Bioinformatics staff and
    students

 

  Human Genome: Data Sources
Starting with the hg19 (GRCh37) assembly, the human genome sequence is
provided by
the Genome Reference Consortium (GRC), whose goal is to correct
the small number of regions in the reference that are currently misrepresented,
to close as many remaining gaps as possible and to produce alternative
assemblies of structurally variant loci when necessary.Prior to hg19, the
human genome sequence data used by the browser were generated by laboratories
belonging to the Human Genome Sequencing Consortium.
Periodic freezes of this data were generated by
NCBI, and EST, mRNA,
BACend and other types of data used for the assembly and annotation were
obtained from GenBank, European Molecular Biology Lab (EMBL), and
DNA Data Bank of Japan (DDBJ).
Clone maps were created by the individual sequencing centers.

The original chromosome files were produced by the institutions and
individuals listed in the table below.

Finished Chromosomes
Chr. # Sequencing Centers AGP File
1 The Sanger Institute, Cambridge, UK

University of Washington, Department of Genome Sciences,
Seattle, WA, USA

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, USABeijing 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, USAStanford Human Genome Center, Palo Alto, CA, USA
Rick Wilson
5 Joint Genome Institute,
U.S. Department of Energy, Walnut Creek, CA, USAStanford 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 USAUniversity 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, UKGesellschaft fuer Biotechnologische Forschung (GBF),
Braunschweig, Germany
Jane Rogers
10 The Wellcome Trust Sanger Institute,
Cambridge, UKGenome 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, FranceInstitute 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, USAStanford 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, USAStanford 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, UKThe University of Oklahoma,
Norman, OK USA

Keio University School of Medicine,
Tokyo, Japan

Jane Rogers
X The Wellcome Trust Sanger Institute,
Cambridge, UKBaylor College of Medicine Human Genome Sequencing Center (BCM-HGSC),
Houston, TX, USA

Institute of Molecular Biology (IMB),
Jena, Germany

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

Max Planck Institute for Molecular Genetics,
Berlin, Germany

Jane Rogers
Y The Genome Institute at Washington University (WUSTL),
St. Louis, MO USA
Rick Wilson

 

 


  Alpaca Genome
The Alpaca Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Alpaca Genome Browser/Initial Annotations:
    • vicPac2:
      Hiram Clawson and Luvina Guruvadoo
    • vicPac1:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

The alpaca data are provided with the following understanding:

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

 


  Armadillo Genome
The Armadillo Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Armadillo Genome Browser/Initial Annotations:
    • dasNov3:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

The armadillo data are provided with the following understanding:

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

 


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



The baboon sequence is made freely available for public use by the
Baboon Genome Sequencing Consortium. Please review the BCM-HGSC
conditions for use guidelines before using this data.

 

  Bonobo Genome
The Bonobo Genome Browser is provided with the following acknowledgments:



The bonobo sequence is made freely available by the
Max-Planck Institute for Evolutionary Anthropology.


  Bushbaby Genome
The Bushbaby Genome Browser is provided with the following acknowledgments:



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

The bushbaby data are provided with the following understanding:

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

 


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

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

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



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

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

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

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

 


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

  • Feb. 2011 panTro4 browser: v2.1.4
    chromosome-based 6X draft assembly
  • Oct. 2010 panTro3 browser: v2.1.3
    chromosome-based 6X draft assembly
  • Mar. 2006 panTro2 browser: v2.1 chromosome-based
    6X draft assembly (Oct. 2005)
  • Nov. 2003 panTro1 browser: v1.1 Arachne draft assembly

The Chimpanzee Genome Browsers have the following acknowledgments:



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



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, Liu X, Li Y, Nagarajan H, Yerganian G, O’Brien E, Bordbar A, Roth AM,
Rosenbloom J, Bian C 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.

 


  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:

  • Jun. 2014 (bosTau8) assembly – UMD CBCB version UMD_3.1.1
  • Oct. 2011 (bosTau7) assembly – Bovine Genome Sequencing Consortium
    (BCM-HGSC) version Btau_4.6.1
  • Nov. 2009 (bosTau6) assembly – UMD CBCB version UMD_3.1
  • Oct. 2007 (bosTau4) assembly – BCM-HGSC version Btau_4.0
  • Aug. 2006 (bosTau3) assembly – BCM-HGSC version Btau_3.1
  • Mar. 2005 (bosTau2) assembly – BCM-HGSC version Btau_2.0
  • Sep. 2004 (bosTau1) assembly – BCM-HGSC version Btau_1.0

The UMD CBCB genome assemblies are provided with the following acknowledgments:

The BCM-HGSC genome assemblies are provided with the following acknowledgments:

  • Funding – For a list of the many agencies that
    funded the cow sequencing project, see the BCM-HGSC
    Bovine Genome Project page.
  • BAC library DNA:
    Dr. Michael MacNeil’s laboratory at the
    USDA Agricultural Research Service,
    Miles City, MT, USA
  • Whole genome shotgun sequence DNA:
    Dr. Timothy Smith’s laboratory at the
    U.S. Meat Animal Research Center,
    Clay Center, NE, USA
  • BAC-based fingerprint map:
    Genome Sciences Centre, Vancouver,
    B.C.
  • UCSC Cow Genome Browser/Initial Annotations:
    • bosTau7:
      Chin Li, Hiram Clawson, Brian Raney and Steve Heitner
    • bosTau4:
      Hiram Clawson, Brian Raney, and Ann Zweig
    • bosTau3:
      Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik
    • bosTau2:
      Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna
      Karolchik
    • bosTau1 (archived):
      Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney,
      Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik


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

UMD cow assembly:

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F,
Pertea G, Van Tassell CP, Sonstegard TS et al.
A whole-genome assembly of the domestic cow, Bos taurus.
Genome Biol. 2009;10(4):R42.

Baylor cow assembly:

Bovine Genome Sequencing and Analysis Consortium.
The genome sequence of taurine cattle: a window to ruminant
biology and evolution
.
Science. 2009 Apr 24;324(5926):522-8.

For more information see the
UMD CBCB
and the BCM-HGSC
Bovine Genome Project pages.

 


  Dog Genome
The UCSC Dog Genome Browser displays assemblies of the domestic dog
(Canis familiaris) with the following acknowledgments:



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
The Dolphin Genome Browser is provided with the following acknowledgments:



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

The dolphin data are provided with the following understanding:

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

 


  Elephant Genome
The elephant assembly was provided by the Broad Institute with the following
acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Elephant Genome Browser/Initial Annotations:
    • loxAfr3: Hiram Clawson, Pauline Fujita, Vanessa Swing,
      Antonio Coelho, and Donna Karolchik


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


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

  • Sequencing/Assembly:
    Ferret Genome Sequencing Consortium and
    The Broad Institute, Cambridge, MA, USA
  • UCSC Ferret Genome Browser/Initial Annotations:
    • musFur1: Hiram Clawson, Brian Lee, and Brooke Rhead


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



The gibbon sequence 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.

 


  Gorilla Genome
The gorilla genome assembly (Gorilla gorilla gorilla) is provided with
the following acknowledgments:



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.

 


  Guinea Pig Genome
The guinea pig assembly (Cavia porcellus) is provided with
the following acknowledgments:



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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Hedgehog Genome
The Hedgehog Genome Browser is provided with the following acknowledgments:

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


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

The hedgehog data are provided with the following understanding:

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

 


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



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



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

The kangaroo rat data are provided with the following understanding:

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

 


  Manatee Genome
The Manatee Genome Browser is provided with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Manatee Genome Browser/Initial Annotations:
    • triMan1:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Marmoset Genome
The Marmoset Genome Browser is provided with the following acknowledgments:


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

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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome.
  4. This is in accordance with, and with the understandings
    in the Fort Lauderdale meeting
    discussing Community Resource Projects and the resulting
    NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.

 


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



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

The megabat data are provided with the following understanding:

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

 


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

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • UCSC Microbat Genome Browser/Initial Annotations:
    • myoLuc2:
      Chin Li, Brian Raney, Robert Kuhn, Steve Heitner, Brooke Rhead, Greg Roe and
      Donna Karolchik


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Minke whale Genome
The minke whale genome is provided by the Korea Institute of Ocean Science and
Technology with the following acknowledgments:



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

Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC,
Kwon KK et al.
Minke whale genome and aquatic adaptation in cetaceans.
Nat Genet. 2014 Jan;46(1):88-92.
PMID: 24270359

 


  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.Prior to mm10/GRCm38, mouse assemblies were produced by the Mouse Genome
Sequencing Consortium, with these acknowledgments:

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



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 Resources Portal.

 


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

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


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

The mouse lemur data are provided with the following understanding:

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

 

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

  • Sequencing/Assembly: Beijing Genomics Institute, Shenzhen, China
  • UCSC Naked Mole-rat Genome Browser/Initial Annotations:
    • hetGla2:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
    • hetGla1:
      Chin Li and Luvina Guruvadoo


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

Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V,
Di Palma F, Lindblad-Toh K, Church GM et al.
The Naked Mole Rat Genome Resource: facilitating analyses of
cancer and longevity-related adaptations
.
Bioinformatics. 2014 Dec 15;30(24):3558-60.

 


  Opossum Genome
The opossum genome assembly (Monodelphis domestica) is provided
by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute,
    Cambridge, MA, USA
  • FISH Mapping:
    North
    Carolina State University
    (NCSU), Raleigh, NC, USA
  • UCSC Opossum Genome Browser/Initial Annotations:
    • monDom5:
      Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and
      Katrina Learned
    • monDom4:
      Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna
      Karolchik
    • monDom1:
      Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna
      Karolchik


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

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M,
Gentles AJ, Goodstadt L, Heger A et al.
Genome of the marsupial Monodelphis domestica reveals innovation
in non-coding sequences
.
Nature. 2007 May 10;447(7141):167-77.

 


  Orangutan Genome
The Sumatran orangutan genome assembly (Pongo pygmaeus abelii) is
provided with the following acknowledgments:

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


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

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP,
Wang Z, Chinwalla AT, Minx P et al.
Comparative and demographic analysis of orang-utan genomes.
Nature. 2011 Jan 27;469(7331):529-33.

 


  Panda Genome
The panda (Ailuropoda melanoleuca) assembly was provided by
BGI-Shenzhen with the following acknowledgments:



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

Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z
et al.
The sequence and de novo assembly of the giant panda genome.
Nature. 2010 Jan 21;463(7279):311-7.
PMID: 20010809

 


  Pig Genome
The pig (Sus scrofa) assembly was provided with the following
acknowledgments:



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 pig genome data is made freely available with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Pika Genome
The pika genome assembly (Ochotona princeps) is provided with
the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Pika Genome Browser/Initial Annotations:
    • ochPri3:
      Hiram Clawson, Brian Raney, and Steve Heitner
    • ochPri2:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

The pika data are provided with the following understanding:

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

 


  Platypus Genome
The platypus genome assembly (Ornithorhynchus anatinus) is provided with the following acknowledgments:



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

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F,
Belov K, Miller W, Clarke L, Chinwalla AT et al.
Genome analysis of the platypus reveals unique signatures of
evolution
.
Nature. 2008 May 8;453(7192):175-83.
PMID: 18464734

 


  Rabbit Genome
The rabbit genome assembly (Oryctolagus cuniculus) is provided with
the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Rabbit Genome Browser/Initial Annotations:
    • oryCun2:
      Hiram Clawson and Antonio Coelho


The rabbit genome data are made freely available before
scientific publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Rat Genome
The rat genome assembly (Rattus norvegicus) is provided by the
Rat Genome Sequencing Consortium with the following acknowledgments:



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

The BGI assembly is provided with the following acknowledgments:

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

The MMGSC assembly is provided with the following acknowledgments:

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

  • UCSC Rhesus Genome Browser/Initial Annotations:
    • rheMac3:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina Guruvadoo, Steve
      Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik
    • rheMac2:
      Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik
    • rheMac1 (archived): Robert Baertsch, Galt Barber, and Donna Karolchik


The initial sequencing and analysis of the rhesus macaque genome
produced by the MMGSC was published in: Rhesus Macaque Genome
Sequencing and Analysis Consortium.
Evolutionary and Biomedical Insights from the Rhesus Macaque
Genome
. Science. 2007 Apr 13;316(5822):222-34.
PMID: 17431167

The initial sequencing and analysis of the rhesus macaque genome produced by
BGI was published in:
Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y,
van Gool AJ et al
Genome sequencing and comparison of two nonhuman primate animal
models, the cynomolgus and Chinese rhesus macaques
. Nat Biotechnol.
2011 Oct 16;29(11):1019-23.
PMID: 22002653

The rhesus macaque sequence is made freely available for public use
with the following understanding:

  1. The data may be freely downloaded, used in analyses,
    and repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider of
    these data is properly acknowledged. For the rheMac1 and rheMac2 data, please
    cite the BCM-HGSC web site or publications from BCM-HGSC referring to
    the genome sequence.
  3. The BCM-HGSC and RMGSC plan to publish the assembly and
    genomic annotation of the dataset, including large-scale
    identification of regions of evolutionary conservation.
  4. This is in accordance with, and with the understandings
    in the Fort Lauderdale meeting discussing
    Community Resource Projects and the resulting
    NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.

 


  Rock Hyrax Genome
The rock hyrax genome assembly (Procavia capensis) is provided with
the following acknowledgments:



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

The rock hyrax data are provided with the following understanding:

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

 


  Sheep Genome
The sheep genome assembly (Ovis aries) is provided by the International
Sheep Genomics Consortium (ISGC) with the following acknowledgments:



The sheep genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite these publications when using these data:

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y,
Zhang W et al.
The sheep genome illuminates biology of the rumen and lipid
metabolism
.
Science. 2014 Jun 6;344(6188):1168-73.
PMID: 24904168

International Sheep Genomics Consortium.
The sheep genome reference sequence: a work in progress.
Anim Genet. 2010 Oct;41(5):449-53.
PMID: 20809919

 


  Shrew Genome
The common shrew genome assembly (Sorex araneus) is provided with
the following acknowledgments:



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

The shrew data are provided with the following understanding:

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

 


  Sloth Genome
The sloth genome assembly (Choloepus hoffmanni) is provided with
the following acknowledgments:



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

The sloth data are provided with the following understanding:

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

 


  Squirrel Genome
The squirrel genome assembly (Spermophilus tridecemlineatus)) is
provided with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Genome Browser/Initial Annotations:
    • speTri2:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

The squirrel data are provided with the following understanding:

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

 


  Squirrel Monkey Genome
The squirrel monkey genome assembly (Saimiri boliviensis) is provided
with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Squirrel Monkey Genome Browser/Initial Annotations:
    • saiBol1:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


The squirrel monkey genome sequence data are made available to the
public with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Tarsier Genome
The tarsier genome assembly (Tarsius syrichta) is provided with
the following acknowledgments:



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

The tarsier data are provided with the following understanding:

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

 


  Tasmanian Devil Genome
The Tasmanian devil genome assembly (Sarcophilus harrisii) is provided
with the following acknowledgments:



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

Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B,
Hims M, Ding Z, Ivakhno S, Stewart C et al.
Genome sequencing and analysis of the Tasmanian devil and its
transmissible cancer
.
Cell. 2012 Feb 17;148(4):780-91.
PMID: 22341448

 

  Tenrec Genome
The tenrec genome assembly (Echinops telfairi) is provided by The
Broad Institute with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Tenrec Genome Browser/Initial Annotations:
    • echTel2:
      Hiram Clawson, Brian Raney and Steve Heitner
    • echTel1:
      Hiram Clawson, Brian Raney and Steve Heitner


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Tree Shrew Genome
The tree shrew genome assembly (Tupaia belangeri) is provided with
the following acknowledgments:



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

The tree shrew data are provided with the following understanding:

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

 


  Wallaby Genome
The wallaby genome assembly (Macropus eugenii) is provided with
the following acknowledgments:



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

Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W,
Waters PD, Pharo EA, Shaw G et al.
Genome sequence of an Australian kangaroo, Macropus eugenii,
provides insight into the evolution of mammalian reproduction and
development
.
Genome Biol. 2011 Aug 29;12(8):R81.
PMID: 21854559

 


  White Rhinoceros Genome
The southern white rhinoceros genome assembly (Ceratotherium simum) is
provided with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • Data Samples:
    Dr. Oliver Ryder, San Diego Zoo Institute for
    Conservation Research, San Diego, CA
  • UCSC White Rhinoceros Genome Browser/Initial Annotations:
    • cerSim1:
      Hiram Clawson and Steve Heitner


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  American Alligator Genome
The American alligator assembly (Alligator mississippiensis) is
provided by the International Crocodilian Genomes Working Group with the
following acknowledgments:



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

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P,
Moran C, Bed’hom B, Abzhanov A et al.
Sequencing three crocodilian genomes to illuminate the evolution
of archosaurs and amniotes
.
Genome Biol. 2012 Jan 31;13(1):415.
PMID: 22293439

 


  Atlantic Cod Genome
The Atlantic cod genome assembly (Gadus morhua) is provided with the
following acknowledgments:

  • Funding:
    Research Council of Norway (FUGE)
  • Sequencing/Assembly:
    GenoFisk Consortium
  • UCSC Atlantic Cod Genome Browser/Initial Annotations:
    • gadMor1:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


The Atlantic cod genome data may be freely downloaded, used in analyses, and
repackaged in databases if the data provider is properly acknowledged. Please
cite these publications when using these data:

Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T,
Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T et al.
Large-scale sequence analyses of Atlantic cod.
N Biotechnol. 2009 Jun;25(5):263-71.
PMID: 19491044

Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF,
Rounge TB, Paulsen J, Solbakken MH, Sharma A et al.
The genome sequence of Atlantic cod reveals a unique immune
system
.
Nature. 2011 Aug 10;477(7363):207-10.
PMID: 21832995

 


  Budgerigar Genome
The budgerigar genome assembly (Melopsittacus undulatus) is provided
with the following acknowledgments:

  • Sequencing/Assembly:
    The Genome Institute at Washington University (WUSTL),
    St. Louis, MO, USA
  • UCSC Budgerigar Genome Browser/Initial Annotations:
    • melUnd1:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome.
  4. This is in accordance with, and with the understandings
    in the Fort Lauderdale meeting
    discussing Community Resource Projects and the resulting
    NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.

 


  Chicken Genome
The chicken genome assembly (Gallus gallus) is provided with
the following acknowledgments:

  • Sequencing:
    The Genome Institute at Washington University (WUSTL),
    St. Louis, MO, USA
  • Physical Map: The Genome Institute at WUSTL
  • Genetic Mapping/Linkage Analysis: The Chicken Mapping Consortium:
    • Wageningen Map based on Wageningen broilerxbroiler mapping population
      (“W” linkage maps; 460 F2 animals), coordinated by Martien Groenen,
      Wageningen University, Wageningen, The Netherlands
    • East Lansing Map based on the RJFxlayer cross (“E” linkage maps; 56 BC
      animals), coordinated by Hans Cheng,
      USDA-ARS, East Lansing, MI, USA
    • Compton map based on layerxlayer cross (“C” linkage maps; 52 BC animals),
      coordinated by Nat Bumstead, Institute for Animal Health
    • Consensus linkage map: Martien Groenen and Richard Crooijmans, Wageningen
      University
    • RH map: coordinated by Mireille Morisson and Alain Vignal,
      French National Institute for Agricultural Research
      (INRA), Toulouse
    • Linkage Mapping: White Leghorn X Red Junglefowl (800 F2 animals),
      coordinated by Susanne Kerje, Lina Jacobsson and Leif Andersson,
      Uppsala University, Uppsala, Sweden
    • Clone/Marker Pairs: coordinated by Jerry Dodgson,
      Michigan State University, East Lansing, MI, USA
    • Marker Name/Sequence Resolution: coordinated by Hans
      Cheng, USDA-ARS, East Lansing, MI, USA
    • Chicken FPC browser:
      ChickFPC, Martien Groenen and Richard
      Crooijmans (galGal3), Jan Aerts (galGal2),
      Wageningen University
    • Additional Mapping Data Contributions: Winston Bellott,
      David Page Lab,
      Whitehead Institute for Biomedical Research (WIBR-MIT),
      Cambridge, MA, USA
  • cDNA sequences: National Institutes of Health and The University of
    Manchester BBSRC ChickEST Database
  • RJF finished clones:
  • Assembly, Assembly/Map Integration, Golden Path
    Creation:
    The Genome Institute at WUSTL
  • SNPs and cross-referenced gene annotations:
    The Beijing Genomics Institute (BGI),
    Beijing, China
  • UCSC Chicken Genome Browser/Initial Annotations:
    • galGal4:
      Hiram Clawson, Brian Raney and Steve Heitner
    • galGal3:
      Angie Hinrichs, Kayla Smith, Donna Karolchik
    • galGal2:
      Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik


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

International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide
unique perspectives on vertebrate evolution
.
Nature. 2004 Dec 9;432(7018):695-716.
PMID: 15592404

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

  1. Users are free to use these data in scientific papers analyzing particular
    genes, if the Beijing Genomics Institute (BGI) is acknowledged.
  2. BGI and its collaborators reserve the right to publish the
    initial analyses of these data, including but not restricted
    to the large-scale identification of functional polymorphisms,
    evolutionary patterns and signs of selection, correlations
    with known QTLs, utility of data for genetic mapping
    purposes, etc.
  3. Any redistribution of these data should carry this notice.

 


  Coelacanth Genome
The coelacanth genome assembly (Latimeria chalumnae) is provided with
the following acknowledgments:



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
The elephant shark genome assembly (Callorhinchus milii) is provided
by the Singapore Institute of Molecular and Cell Biology with the following
acknowledgments:



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

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF,
Sutoh Y, Kasahara M et al.
Elephant shark genome provides unique insights into gnathostome
evolution
.
Nature. 2014 Jan 9;505(7482):174-9.
PMID: 24402279

 


  Fugu Genome
The Fugu genome assembly (Takifugu rubripes) is provided by the
U.S. DOE Joint Genome Institute (JGI) as
part of the International Fugu Genome Consortium, led by the JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
The assembly has the following acknowledgments:

  • Sequencing/Assembly:
    Assembly was constructed with the JGI assembler, JAZZ, from paired end
    sequencing reads produced by JGI and the IMCB at JGI, Myriad Genetics, and
    Celera Genomics
  • UCSC Fugu Genome Browser/Initial Annotations:
    • fr3:
      Hiram Clawson and Greg Roe
    • fr2:
      Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik
    • fr1:
      Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik


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

Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H,
Naruse K, Brenner S et al.
Integration of the genetic map and genome assembly of fugu
facilitates insights into distinct features of genome evolution in teleosts and
mammals
.
Genome Biol Evol. 2011;3:424-42.
PMID: 21551351

 


  Lamprey Genome
The lamprey genome assembly (Petromyzon marinus) is provided with
the following acknowledgments:



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

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD,
Manousaki T, Meyer A et al.
Sequencing of the sea lamprey (Petromyzon marinus) genome
provides insights into vertebrate evolution
.
Nat Genet. 2013 Apr;45(4):415-21, 421e1-2.
PMID: 234350859

 


  Lizard Genome
The lizard genome assembly (Anolis carolinensis) is provided by The
Broad Institute with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA USA
  • UCSC Lizard Genome Browser/Initial Annotations:
    • anoCar2:
      Hiram Clawson, Brian Raney, Luvina Guruvadoo, and Donna Karolchik
    • anoCar1:
      Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik


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

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E,
Russell P, Lowe CB, Glor RE, Jaffe JD et al.
The genome of the green anole lizard and a comparative analysis
with birds and mammals
.
Nature. 2011 Aug 31;477(7366):587-91.
PMID: 21881562

 


  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/Initial Annotations:
    • oryLat2:
      Hiram Clawson, Pauline Fujita, and Donna Karolchik


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

Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y,
Doi K, Kasai Y et al.
The medaka draft genome and insights into vertebrate genome
evolution
.
Nature. 2007 Jun 7;447(7145):714-9.
PMID: 17554307

 


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

  • Sequencing/Assembly: Genome 10K Project and Beijing Genomics
    Institute (BGI)
  • UCSC Medium Ground Finch Genome Browser/Initial Annotations:
    • geoFor1:
      Hiram Clawson and Greg Roe


The medium ground finch sequence is made freely available before scientific
publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Nile Tilapia Genome
The Nile tilapia genome assembly (Oreochromis niloticus) is provided
with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA, USA
  • UCSC Nile Tilapia Genome Browser/Initial Annotations:
    • oreNil2:
      Hiram Clawson, Chin Li, Brian Raney, Pauline Fujita, Luvina
      Guruvadoo, Steve Heitner, Brooke Rhead, Greg Roe, and Donna Karolchik


The Nile Tilapia genome sequence data are made available to the
public with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 

  Painted Turtle Genome
The painted turtle genome assembly (Chrysemys picta bellii) is provided
with the following acknowledgments:

  • Sequencing/Assembly: International Painted Turtle Genome Sequencing
    Consortium
  • UCSC Painted Turtle Genome Browser/Initial Annotations:
    • chrPic1:
      Hiram Clawson, Brian Raney and Steve Heitner


The painted turtle genome sequence data are made available to the
public with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Stickleback Genome
The stickleback genome assembly (Gasterosteus aculeatus) is provided
by The Broad Institute with the following acknowledgments:

  • Sequencing/Assembly:
    The Broad Institute, Cambridge, MA USA
  • UCSC Stickleback Genome Browser/Initial Annotations:
    • gasAcu1:
      Angie Hinrichs, Hiram Clawson, Kayla Smith, and Donna Karolchik


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Tetraodon Genome
The Tetraodon genome assembly (Tetraodon nigroviridis) is provided with
the following acknowledgments:


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.

 


  Turkey Genome
The turkey genome assembly (Meleagris gallopavo) is provided with
the following acknowledgments:



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

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann,
Bouffard P, Burt DW, Crasta O, Crooijmans RP et al.
Multi-platform next-generation sequencing of the domestic turkey
(Meleagris gallopavo): genome assembly and analysis
.
PLoS Biol. 2010 Sep 7;8(9).
PMID: 20838655

 


  X. tropicalis Genome
The Xenopus (Silurana) tropicalis genome assembly is provided by the
U.S. DOE Joint Genome Institute (JGI)
with the following acknowledgments:

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

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

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V,
Ovcharenko I, Putnam NH, Shu S, Taher L et al.
The genome of the Western clawed frog Xenopus tropicalis.
Science. 2010 Apr 30;328(5978):633-6.
PMID: 20431018

 


  Zebra Finch Genome
The zebra finch genome assembly (Taeniopygia guttata) is
provided by the Genome Institute at Washington University (WUSTL)
with the following acknowledgments:

  • Sequencing/Assembly:
    The Genome Institute at WUSTL, St. Louis, MO, USA
  • Zebra finch DNA:
    Arthur P. Arnold lab, Dept. of Physiological Science,
    UCLA, Los Angeles, CA, USA
  • UCSC Zebra Finch Genome Browser/Initial Annotation:
    • taeGut2:
      Hiram Clawson, Brian Raney, and Steve Heitner
    • taeGut1:
      Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik


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

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A,
Searle S, White S, Vilella AJ, Fairley S et al.
The genome of a songbird.
Nature. 2010 Apr 1;464(7289):757-62.
PMID: 20360741

 


  Zebrafish Genome
Starting with the danRer10 (GRCz10) assembly, the zebrafish genome sequence is
now provided by the
Genome Reference Consortium (GRC).Prior assemblies have the following acknowledgments:

  • Sequencing/Assembly:
    The Wellcome Trust Sanger Institute, UK.
  • FPC map:
  • BAC Clones, BAC End Pairs:
    • The Wellcome Trust Sanger Institute, UK – GenBank
      accessions for BAC clones
    • Max-Planck Institute for Developmental
      Biology, Germany – BAC end pairs sequence data
    • Hubrecht Laboratory, Netherlands Institute
      for Developmental Biology, The Netherlands – BAC end pairs
      sequence data
  • Annotations:
  • UCSC Zebrafish Genome Browsers:
    • danRer10: Hiram Clawson, Brian Raney, Steve Heitner
    • danRer7: Hiram Clawson, Mary Goldman, Greg Roe, Brian
      Raney, Donna Karolchik
    • danRer6: Galt Barber, Robert Kuhn, Katrina Learned,
      Donna Karolchik
    • danRer5: Rachel Harte, Ann Zweig, Donna Karolchik
    • danRer4: Rachel Harte, Archana Thakkapallayil, Robert
      Kuhn, Ann Zweig, Donna Karolchik
    • danRer3: Rachel Harte, Jennifer Jackson, Ann Zweig,
      Ali Sultan-Qurraie, Donna Karolchik
    • danRer2 (archived): Rachel Harte,
      Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson

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

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE,
Humphray S, McLaren K, Matthews L et al.
The zebrafish reference genome sequence and its relationship
to the human genome
.
Nature. 2013 Apr 25;496(7446):498-503.
PMID: 23594743

For more information about zebrafish assemblies provided by the GRC, see the
GRC zebrafish web pages. For information about assemblies
prior to danRer10/GRCz10, see the Sanger Institute’s
Danio rerio Sequencing Project web page.

 

  C. intestinalis Genome
The C. intestinalis v1.0 and v2.0 draft assemblies are provided
by the U.S. DOE Joint Genome Institute (JGI) with the
following acknowledgments:


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
The lancelet (Branchiostoma floridae) genome assembly is provided
by the DOE Joint Genome Institute (JGI) with the following acknowledgments:

  • Funding:
    U.S. Department of Energy Office of Science, Biological
    and Environmental Research Program
  • Sequencing/Assembly:
    JGI
  • UCSC Lancelet Genome Browser/Initial Annotations:
    • braFlo1:
      Hiram Clawson, Ann Zweig, Pauline Fujita, Donna Karolchik

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

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T,
Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK et al.
The amphioxus genome and the evolution of the chordate
karyotype
.
Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.
PMID: 18563158

 


  S. purpuratus Genome
The sea urchin (Strongylocentrotus purpuratus) genome assembly
is provided by the Baylor College of Medicine Human Genome Sequencing Center
(BCM-HGSC). The assemblies available in the browser include:

  • Sep. 2006 strPur2 browser: Baylor version Spur 2.1 (NCBI v2.1)
  • Apr. 2005 strPur1 browser: Baylor version Spur_0.5 (NCBI v1.1)

These data are provided with the following acknowledgments:

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

Sea Urchin Genome Sequencing Consortium.
The genome of the sea urchin Strongylocentrotus purpuratus.
Science. 2006 Nov 10;314(5801):941-52.
PMID: 17095691

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

 


  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:


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


The A. mellifera sequence is made freely available
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). The D. ananassae
Genome Browser has the following acknowledgments:

  • Sequencing:
    Agencourt Bioscience,
    Danvers, MA, USA
  • Assembly:
  • UCSC D. ananassae Genome Browser (droAna2):
    Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith, and
    Donna Karolchik
  • UCSC D. ananassae Genome Browser (droAna1):
    Angie Hinrichs, Brian Raney, Heather Trumbower, Ali
    Sultan-Qurraie, and Donna Karolchik
  • Initial Genome Browser Annotations:
    UCSC Genome
    Bioinformatics Group
    , University of California,
    Santa Cruz, CA, USA

These data have been freely provided by Agencourt
Bioscience before
publication for use in the UCSC Genome Browser with the
following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the
    provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial
    large-scale analyses of the dataset, including large-scale
    identification of regions of evolutionary conservation and
    large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

 



  D. erecta Genome
The droEre1 data were provided by
Agencourt Bioscience. The
D. erecta Genome Browser has the following
acknowledgments:


These data have been freely provided by Agencourt
Bioscience before
publication for use in the UCSC Genome Browser with the
following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the
    provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial
    large-scale analyses of the dataset, including large-scale
    identification of regions of evolutionary conservation and
    large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

 



  D. grimshawi Genome
The droGri data were provided by
Agencourt Bioscience. The
D. grimshawi Genome Browser has the following
acknowledgments:

  • Sequencing and Assembly:
    Agencourt Bioscience,
    Danvers, MA, USA, using the
    Arachne assembler
  • UCSC D. grimshawi Genome Browser (droGri1):
    Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith
    and Donna Karolchik
  • Initial Genome Browser Annotations:
    UCSC Genome
    Bioinformatics Group
    , University of California,
    Santa Cruz, CA, USA

These data have been freely provided by Agencourt
Bioscience before
publication for use in the UCSC Genome Browser with the
following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the
    provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial
    large-scale analyses of the dataset, including large-scale
    identification of regions of evolutionary conservation and
    large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

 



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

  • Sequencing and Assembly:
  • Annotations:
    • Euchromatic regions –
      FlyBase
    • Heterochromatic regions –
      DHGP, Lawrence Berkeley
      National Laboratory, Berkeley, CA, USA
  • UCSC D. melanogaster Genome Browser
    and additional annotations (dm6):

    Hiram Clawson, Angie Hinrichs, and Matthew Speir
  • UCSC D. melanogaster Genome Browser
    and additional annotations (dm3):

    Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and
    Donna Karolchik –
    UCSC Genome
    Bioinformatics Group
    , UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster Genome Browser
    and additional annotations (dm2):

    Angie Hinrichs, Brian Raney, Galt Barber,
    and Donna Karolchik –
    UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster Genome Browser
    and additional annotations (dm1):

    Angie Hinrichs, Brian Raney, Heather Trumbower, Ali
    Sultan-Qurraie, and Donna Karolchik –
    UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA

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

 



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


These data have been freely provided by Agencourt
Bioscience before
publication for use in the UCSC Genome Browser with the
following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the
    provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial
    large-scale analyses of the dataset, including large-scale
    identification of regions of evolutionary conservation and
    large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

 


  D. persimilis Genome
The droPer1 assembly was provided with the following acknowledgments:

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


The D. persimilis sequence is made freely available
before scientific
publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 



  D. pseudoobscura Genome
These data were produced by the
Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC).
The D. pseudoobscura Genome Browser has the following
acknowledgments:

  • Sequencing and Assembly:
    BCM-HGSC, Houston, TX, USA
  • UCSC D. pseudoobscura Genome Browser (dp3):
    Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna
    Karolchik
  • UCSC D. pseudoobscura Genome Browser (dp2):
    Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna
    Karolchik
  • Initial Genome Browser Annotations:
    UCSC Genome
    Bioinformatics Group
    , University of California,
    Santa Cruz, CA, USA

The D. pseudoobscura data are made available with
specific conditions for use.

 


  D. sechellia Genome
The droSec1 assembly was provided with the following acknowledgments:



The D. sechellia sequence is made freely available
before scientific
publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 



  D. simulans Genome
These data were provided with the following acknowledgments:


The D. simulans sequence is made freely available before
scientific publication with the following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome.
  4. This is in accordance with, and with the understandings
    in the Fort Lauderdale meeting
    discussing Community Resource Projects and the resulting
    NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.

 



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


These data have been freely provided by Agencourt
Bioscience before
publication for use in the UCSC Genome Browser with the
following understanding:

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the
    provider of these data is properly acknowledged.
  3. Agencourt Bioscience reserves the right to publish the initial
    large-scale analyses of the dataset, including large-scale
    identification of regions of evolutionary conservation and
    large-scale genomic assembly.
  4. Any redistribution of the data should carry this notice.

 



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


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

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

 



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

 



  Worm Genomes (other than C. elegans)
The latest versions of the C. brenneri,
C. briggsae, C. japonica,
C. remanei, and P. pacificus sequences
were obtained from the Genome Sequencing Center at
The Genome Institute at Washington University (WUSTL).
The cb1 browser data
were obtained from WormBase.We’d like to thank WUSTL for providing the sequence data
for these assemblies, as well as the Sanger Institute for
their collaborative work in sequencing the initial
C. briggsae cb1 genome. Thanks also to the
WormBase consortium for providing access to the cb1
sequence.


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The centers producing the data reserve the right to
    publish the initial large-scale analyses of the data set,
    including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome.
  4. This is in accordance with, and with the understandings
    in the Fort Lauderdale meeting
    discussing Community Resource Projects and the resulting
    NHGRI policy statement.
  5. Any redistribution of the data should carry this notice.

 



  Yeast Genome
UCSC Sacchromyces cerevisiae Genome Browser (sacCer3): Hiram Clawson,
Greg Roe, Steve Heitner.
The April 2011 Sacchromyces cerevisiae genome assembly
is based on sequence dated April 2011 in the
Sacchromyces Genome
Database
(SGD). This genome sequence was downloaded from
NCBI (genbank/genomes/Eukaryotes/fungi/Saccharomy
ces_cerevisiae/SacCer_Apr2011/). The SGD™ gene annotations were downloaded
from the SGD downloads site. The S288C strain was used in this sequencing project.The June 2008 Sacchromyces cerevisiae genome assembly
(sacCer2)

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

The Oct. 2003 Sacchromyces cerevisiae genome assembly
(sacCer1)

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

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

 


  California Sea Hare Genome
The Aplysia californica genome assembly
has the following acknowledgments:

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


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

  1. The data may be freely downloaded, used in analyses, and
    repackaged in databases.
  2. Users are free to use the data in scientific papers
    analyzing particular genes and regions if the provider
    of these data is properly acknowledged.
  3. The center producing the data reserves the right to
    publish the initial large-scale analyses of the data
    set, including large-scale identification of regions of
    evolutionary conservation and large-scale genomic
    assembly. Large-scale refers to regions with size on the
    order of a chromosome (that is, 30 Mb or more).
  4. Any redistribution of the data should carry this notice.

 


  Ebola Virus Genome
The Ebola virus genome assembly
has the following acknowledgments:

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

Other Acknowledgements:

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

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



The Ebola virus sequence may be freely downloaded, used in analyses,
and repackaged in databases. The data may be freely used in scientific
papers analyzing particular genes and regions if the provider of these
data is properly acknowledged.

 


  External Contributors
to the UCSC Genome Browser Project

 


  Acknowledgment of Early Support
During the initial stage of this project, from January 2000 to June 2001,
we received no direct federal funding to develop the working draft other than
travel support. However, we gratefully acknowledge the support for our
personnel provided by our basic bioinformatics research grants, especially
DOE grant DE-FG03-99ER62849 (to develop gene-finding methods), but also NSF
grant DBI-9809007, UC BIOTECH grant 99-11, a grant from the Sloan Foundation,
the David and Lucille Packard Foundation, NIH grant GM-52848, and the Zahler
grant that provided support for Jim Kent in the early stages of this work.We are particularly thankful for the risks that Patrick Mantey (UCSC Dean of
Engineering), James Gill (Vice Chancellor for Research), John Simpson (UCSC
Provost), and M.R.C. Greenwood (UCSC Chancellor) were willing to take
in advancing us the money in February 2000 needed to build the original
100-node LINUX cluster used in this work, and in the case of Dean Mantey,
additional personnel support. Phokion Kolaitis, Chair of Computer Science,
contributed as well.

 

 

 

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