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  UCSC Genome Browser Acknowledgments

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

Click here to view the contributions of the UCSC Genome Browser project team.



  Human Genome: Acknowledgements
HHMI CISI
NHGRI

The UCSC Human Genome Browser Project is conducted in collaboration with the International Human Genome Project. We have worked with many collaborators at other institutions to produce and annotate this reference sequence of the human genome, as described in our recent publications. The UCSC Human Genome Project is made possible by a grant from the National Human Genome Research Institute, directed by Francis Collins, and generous support from the Howard Hughes Medical Institute and the California Institutes for Science and Innovation.

The Human Genome Browser is produced by the UCSC Genome Bioinformatics Group. Annotations are produced by UCSC and collaborators at other institutions. To review the acknowledgements for an annotation, consult the "Credits" section on the annotation track's description page in the Genome Browser.

The hg18 UCSC Genome Browser was produced by the UCSC Genome Browser staff.



  Human Genome: Data Sources

The human genome sequence data we use have been generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data are generated by NCBI. EST, mRNA, BACend and other types of data used for the assembly and annotation are taken from GenBank /EMBL /DDBJ. Clone maps were created by the individual sequencing centers.

The assembly of the finished chromosomes is taken directly from files edited by Greg Schuler at NCBI. The original files are produced by the institutions and people listed in the table below.

Finished Chromosomes
Chr. # Sequencing Centers AGP File
1 Jane Rogers
2 Rick Wilson
3 Steve Scherer
4 Rick Wilson
5 Jeremy Schmutz
6 Jane Rogers
7 Rick Wilson
8 Chad Nusbaum
9 Jane Rogers
10 Jane Rogers
11 Todd Taylor
12 Steve Scherer
13 Jane Rogers
14 Jean Weissenbach
15 Chad Nusbaum
16 Jeremy Schmutz
17 Chad Nusbaum
18 Chad Nusbaum
19 Jeremy Schmutz
20 James Gilbert
21 Todd Taylor
22 Jane Rogers
X Jane Rogers
Y Rick Wilson



  Chimpanzee Genome

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

  • Mar. 2006 panTro2 browser: Build 2, Version 1 chromosome-based assembly based on data from the Oct. 2005 6X draft assembly
  • Nov. 2003 panTro1 browser: Build 1, Version 1 Arachne draft assembly
The Chimp Genome Browsers have the the following acknowledgements:

The chimpanzee sequence is made freely available before scientific publication from the Chimpanzee Genome Sequencing Consortium with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (the Chimpanzee Genome Sequencing Consortium) are 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.


  Rhesus Genome

The sequencing and assembly of the Macaca mulatta genome is a project of the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the J. Craig Venter Institute Joint Technology Center, and the Genome Sequencing Center at Washington University School of Medicine, St. Louis.

  • Jan. 2006 rheMac2 Genome Browser: Jan. 2006 draft assembly of the rhesus monkey, version Mmul_051212 from Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC)
  • Jan. 2005 rheMac1 Genome Browser: Jan. 2005 draft assembly of the rhesus monkey, version Mmul_0.1.

This assembly is provided with the following acknowledgements:

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

These data are made available before scientific publication with the following understanding:
  • The data may be freely downloaded, used in analyses, and repackaged in databases.
  • Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (Baylor College of Medicine Human Genome Sequencing Center and the Rhesus Macaque Genome Sequencing Consortium) are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence.
  • 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.
  • This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.
  • Any redistribution of the data should carry this notice.


  Cat Genome

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

The cat 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 providers of these data (The Broad Institute and Agencourt Bioscience) are 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.


  Dog Genome

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

The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite the following publication when using these data:

Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438:803-19.


  Cow Genome

The UCSC Cow Genome Browser displays data obtained from the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC):

  • Oct. 2007 (bosTau4) assembly - based on Baylor version Btau_4.0
  • Aug. 2006 (bosTau3) assembly - based on Baylor version Btau_3.1
  • Mar. 2005 (bosTau2) assembly - based on Baylor version Btau_2.0
  • Sep. 2004 (bosTau1) assembly - based on Baylor version Btau_1.0.

These data are provided with the following acknowledgements:

  • Funding - For a list of the many agencies that funded the cow sequencing project, see the BCM HGSC web page.
  • Sequencing/Assembly: BCM HGSC, Houston, TX, USA
  • 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 (bosTau4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Brian Raney, and Ann Zweig.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna Karolchik.
  • UCSC Cow Genome Browser/Initial Annotations (bosTau1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik.

For more information on the bovine genome project, see the BCM HGSC Bovine Genome Project web page.

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


  Mouse Genome

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

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

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

Mouse genome sequence data are released weekly into a public repository maintained by EBI and NCBI. References to these data should cite the following publication: Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562 (2002).

  Rat Genome

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

The Rat genome sequence was produced with the following acknowledgements:

The rat genome sequence is made freely available by the Rat Genome Project at the Baylor College of Medicine Human Genome Sequencing Center. Please cite the following publications when using these data:

Havlak, P. et al. The Atlas genome assembly system. Genome Res. 14(4), 721-32 (2004).

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982), 493-521 (2004).

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


  Opossum Genome

The UCSC Opossum Genome Browser displays data from the draft assemblies of the opossum (Monodelphis domestica) produced by The Broad Institute. These assemblies are provided with the following acknowledgements:

  • Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  • FISH Mapping: North Carolina State University (NCSU), Raleigh, NC, USA
  • UCSC Opossum Genome Browser/Initial Annotations (monDom4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik
  • UCSC Opossum Genome Browser/Initial Annotations (monDom1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik

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


  Orangutan Genome

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

The orangutan sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (Genome Sequencing Center at WUSTL) 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.


  Guinea Pig Genome

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

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 (The Broad Institute) 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.


  Horse Genome

The UCSC Horse Genome Browser displays data from the Jan. 2007 EquCab1 draft assembly of the horse (Equus caballus) from The Broad Institute. This assembly is provided with the following acknowledgements:

The horse sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) 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.


  Platypus Genome

The platypus Genome Browser was produced with the following acknowledgements:

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

The platypus sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data are properly acknowledged. See the WUSTL website for credit information.
  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. 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 sequence was produced with the following acknowledgements:

  • Sequencing: The Genome Sequencing Center at Washington University School of Medicine, St. Louis, MO, USA (WUSTL)
  • Physical Map: 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 (see the Chick RH Server)
    • 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: WUSTL
  • SNPs and cross-referenced gene annotations: The Beijing Genomics Institute (BGI), Beijing, China
  • UCSC Chicken Genome Browser (galGal3): Angie Hinrichs, Kayla Smith, Donna Karolchik
  • UCSC Chicken Genome Browser (galGal2): Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik

The G. gallus sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, 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 providers of this data (Genome Sequencing Center, Washington University School of Medicine) are properly cited:
    International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004 Dec 9;432(7018): 695-716. PMID: 15592404.
  3. Any redistribution of the data should carry this notice.

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

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

  X. tropicalis Genome

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

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

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

  Zebrafish Genome

The zebrafish draft assemblies were provided by The Wellcome Trust Sanger Institute. The UCSC Zebrafish Genome Browser has the following acknowledgements:

  • Sequencing/Assembly: The Wellcome Trust Sanger Institute, UK.
  • FPC map:
  • BAC Clones, BAC End Pairs:
    • The Wellcome Trust Sanger Institute, UK - GenBank accessions for BAC clones
    • Max-Planck Institute for Developmental Biology, Germany - BAC end pairs sequence data
    • Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands - BAC end pairs sequence data
  • Initial Annotations:
  • UCSC Zebrafish Genome Browser (danRer5): Rachel Harte, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer4): Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer3): Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer2): Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson

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

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


  Tetraodon Genome

The Tetraodon nigroviridis V7 assembly (February 2004) was provided by Genoscope in collaboration with The Broad Institute. This assembly has the following acknowledgements:

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

  Fugu Genome

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

  • 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 (fr2) Genome Browser: Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik
  • UCSC Fugu (fr1) Genome Browser: Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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


  Lamprey Genome

The lamprey assembly was provided by the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements:

The lamprey sequence is made freely available before scientific publication. Please see the WUSTL data use policy for usage restrictions and citation information.


  Lancelet Genome

The lancelet assembly was provided by the DOE Joint Genome Institute (JGI) with the following acknowledgements:

  • Funding: U.S. Department of Energy Office of Science, Biological and Environmental Research Program
  • Sequencing/Assembly: JGI
  • UCSC Lancelet (braFlo1) Genome Browser: Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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


  Lizard Genome

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

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

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


  Stickleback Genome

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

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

The stickleback sequence is made freely available before scientific publication with the following understanding:
  1. The data may be freely downloaded, used in analyses, and repackaged in databases.
  2. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) 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

These data were provided by the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements:

These data were produced by the Genome Sequencing Center, WUSTL School of Medicine and can be obtained from http://genome.wustl.edu/pub/organism/Primates/Callithrix_jacchus/assembly/Callithrix_jacchus-2.0.2/. It is requested that users of this marmoset sequence assembly acknowledge the Washington University School of Medicine, Genome Sequencing Center in any publications that result from use of this sequence assembly. If you have any questions regarding the use of these data, please contact WUSTL at webmaster@genome.wustl.edu. Contact the Director of the Sequencing Center, Richard Wilson, before publishing analyses of the sequence on a chromosome or genome scale. WUSTL welcomes collaborative interaction to provide the community with improved whole genome analyses and annotations. See the WUSTL data use policy for more information.


  Medaka Genome

The Medaka whole genome shotgun assembly was provided by Japan's National Institute of Genetics (NIG) and the University of Tokyo. The assembly was constructed using the RAMEN assembler.

  • Sequencing/Assembly: NIG and University of Tokyo, Japan
  • UCSC Medaka (oryLat1) Genome Browser: Hiram Clawson, Brian Raney, Archana Thakkapallayil, and Donna Karolchik
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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


  C. Intestinalis Genome

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

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


  S. purpuratus Genome

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

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

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

  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 acknowledgements:

  • Sequencing and Assembly:
  • Annotations:
    • Euchromatic regions - FlyBase
    • Heterochromatic regions - DHGP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • UCSC D. melanogaster (dm3) Genome Browser and additional annotations: Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster (dm2) Genome Browser and additional annotations: Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA
  • UCSC D. melanogaster (dm1) Genome Browser and additional annotations: 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. ananassae Genome

The droAna2 data were provided by Agencourt Bioscience Corporation. The droAna1 data were produced by the Institute for Genomic Research (TIGR). The D. ananassae Genome Browser has the following acknowledgements:

  • Sequencing: Agencourt Bioscience Corporation, Beverly, MA, USA
  • Assembly:
  • UCSC D. ananassae (droAna2) Genome Browser: Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith, and Donna Karolchik
  • UCSC D. ananassae (droAna1) Genome Browser: 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 Corporation 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, provided that the Agencourt is properly acknowledged.
  3. Agencourt 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.

Please contact Douglas R. Smith at Agencourt with questions concerning these data.


  D. persimilis Genome

The droPer1 assembly was provided by the Broad Institute with the following acknowledgements:

  • Sequencing/Assembly: The Broad Institute
  • UCSC D. persimilis (droPer1) Genome Browser: 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 (The Broad Institute) 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. erecta Genome
The droEre1 data were provided by Agencourt Bioscience Corporation. The D. erecta Genome Browser has the following acknowledgements:

These data have been freely provided by Agencourt Bioscience Corporation 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, provided that the Agencourt is properly acknowledged.
  3. Agencourt 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.

Please contact Douglas R. Smith at Agencourt with questions concerning these data.


  D. simulans Genome

These data were provided by the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements:

The D. simulans sequence is made freely available before scientific publication by the Genome Sequencing Center, 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 providers of these data (Genome Sequencing Center, WUSTL School of Medicine) are properly acknowledged.
  3. The Drosophila simulans analysis group is aiming to publish an initial analysis of the D. simulans 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.

  D. sechellia Genome

The droSec1 assembly was provided by the Broad Institute with the following acknowledgements:

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 (The Broad Institute) 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. yakuba Genome

These data were provided by the Genome Sequencing Center at Washington University (WUSTL) School of Medicine, St. Louis with the following acknowledgements:

The D. yakuba sequence is made freely available before scientific publication by the Genome Sequencing Center, 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 providers of these data (Genome Sequencing Center, WUSTL School of Medicine) are 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.

  D. virilis Genome

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

These data have been freely provided by Agencourt Bioscience Corporation 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, provided that the Agencourt is properly acknowledged.
  3. Agencourt 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.

Please contact Douglas R. Smith at Agencourt with questions concerning these data.


  D. mojavensis Genome

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

These data have been freely provided by Agencourt Bioscience Corporation 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, provided that the Agencourt is properly acknowledged.
  3. Agencourt 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.

Please contact Douglas R. Smith at Agencourt with questions concerning these data.


  D. pseudoobscura Genome

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

  • Sequencing and Assembly: Baylor College of Medicine HGSC
  • UCSC D. pseudoobscura (dp3) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik
  • UCSC D. pseudoobscura (dp2) Genome Browser: 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. grimshawi Genome
The droGri data were provided by Agencourt Bioscience Corporation. The D. grimshawi Genome Browser has the following acknowledgements:

These data have been freely provided by Agencourt Bioscience Corporation 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, provided that the Agencourt is properly acknowledged.
  3. Agencourt 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.

Please contact Douglas R. Smith at Agencourt with questions concerning these data.


  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 acknowledgements: