UCSC Genome Bioinformatics
  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 UCSC Human Genome Browser is generated by the UCSC Genome Bioinformatics Group, and annotations are produced by UCSC and collaborators at other institutions. The UCSC staff responsible for producing the initial hg19 browser include Hiram Clawson, Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned, and Robert Kuhn. To view complete acknowledgements for a specific annotation, see the "Credits" section on the annotation track's description page in the Genome Browser.



  Human Genome: Data Sources

Starting with the hg19 assembly, the human genome sequence is provided by the Genome Reference Consortium (GRC), whose goal is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary.

Prior to hg19, the human genome sequence data used in the browser were generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data were generated by NCBI, and EST, mRNA, BACend and other types of data used for the assembly and annotation were obtained from GenBank /EMBL /DDBJ. Clone maps were created by the individual sequencing centers.

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

Finished Chromosomes
Chr. # Sequencing Centers AGP File
1 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 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 was produced with the following acknowledgements:

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 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 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 (monDom5): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and Katrina Learned
  • UCSC Opossum Genome Browser/Initial Annotations (monDom4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik
  • UCSC Opossum Genome Browser/Initial Annotations (monDom1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik


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 the draft assembly of the horse (Equus caballus) genome 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.


  Panda Genome

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


The panda 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 (BGI-Shenzhen) 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.


  Pig Genome

The pig assembly was provided by NCBI with the following acknowledgements:


The pig 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. 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.


  Rabbit Genome

The rabbit Genome Browser was produced with the following acknowledgements:

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


The rabbit 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) 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.


  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.

  Zebra Finch Genome

The zebra finch draft assembly was obtained from the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements:

  • Sequencing/Assembly: 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 (taeGut1): Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik
  • Initial Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA


The zebra finch sequence is made freely available to the community by the Genome Sequencing Center at the WUSTL 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 these data if the providers of these data are properly acknowledged. See http://genome.wustl.edu/data.cgi 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.
  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.
Please refer to the WUSTL data use policy for additional usage guidelines and citation information.

  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 (danRer6): Galt Barber, Robert Kuhn, Katrina Learned, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer5): Rachel Harte, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer4): Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer3): Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, Donna Karolchik
  • UCSC Zebrafish Genome Browser (danRer2): Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson


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

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


  Tetraodon Genome

The Tetraodon nigroviridis assemblies have been provided with 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).

  Elephant Genome

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

  • Sequencing/Assembly: The Broad Institute
  • UCSC Elephant (loxAfr3) Genome Browser: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik.
  • Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA


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 (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.


  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 Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements:


These data were produced by the Genome Center at the WUSTL School of Medicine and can be obtained from their downloads page. Please review the Genome Center's data use policy before using these data in publications. If you have any questions regarding the use of these data, please contact WUSTL at webmaster@genome.wustl.edu.

  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.

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 (oryLat2) Genome Browser: Hiram Clawson, Pauline Fujita, 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:


The A. mellifera sequence is made freely available before scientific publication by the BCM HGSC. See the Baylor conditions of use statement for guidelines regarding the use of these data.

  A. gambiae Genome

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


The A. gambaie sequence is made freely available by The International Anopheles Genome Project.

  C. elegans Genome

The C. elegans data was obtained from WormBase. We'd like to thank the Genome Sequencing Center at Washington University in St. Louis 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 Washington University in St. Louis (WUSTL) School of Medicine. The cb1 browser data were obtained from WormBase. Please review the WUSTL data use policy before using these data in research or a publication.

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.


  Yeast Genome

The June 2008 Sacchromyces cerevisiae genome assembly 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 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 ftp://genome-ftp.stanford.edu/pub/yeast/data_download. 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 acknowledgements:

  • Sequencing and 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 (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.


  External Contributors to the UCSC Genome Browser Project

  Acknowledgements of Early Support

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

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

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

Beginning in December, 2000, we started to utilize some support from HHMI for equipment and personnel. In the summer of 2001, HHMI provided the primary funding for a new cluster of 1000 CPUs running LINUX purchased from Rackable, with additional support from CISI and NHGRI. Dubbed the UCSC KiloKluster, this equipment now provides the computational backbone for the project.