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

• Human Genome
• Chimpanzee Genome
• Dog Genome
• Cow Genome
• Mouse Genome
• Rat Genome
• Opossum Genome
• Chicken Genome
• X. tropicalis Genome
• Zebrafish Genome
• Tetraodon Genome
• Fugu Genome
• C. intestinalis Genome
• D. melanogaster Genome
• D. yakuba Genome
• D. ananassae Genome
• D. pseudoobscura Genome
• D. virilis Genome
• D. mojavensis Genome
• A. mellifera Genome
• A. gambiae Genome
• C. elegans Genome
• C. briggsae Genome
• Yeast Genome
• SARS Genome
• NISC Comparative Sequencing Program Data
• Other scientists featured on this site
• Acknowledgements of early support

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

The UCSC Human Genome 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 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 The Sanger Institute, Cambridge, UK. University of Washington Genome Center, Seattle, WA, USA Jane Rogers 2 Washington University School of Medicine Genome Sequencing Center, St Louis, MO, USA Rick Wilson 3 Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Beijing Human Genome Center, Beijing, China University of Washington Genome Center, Seattle, WA, USA Steve Scherer 4 Washington University School of Medicine Genome Sequencing Center, St Louis, MO, USA Stanford Human Genome Center, Palo Alto, CA, USA Rick Wilson 5 Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center (Myers), Palo Alto, CA, USA Jeremy Schmutz 6 The Sanger Institute, Cambridge, UK. Jane Rogers 7 Washington University School of Medicine Genome Sequencing Center, St Louis, USA University of Washington Genome Center, Seattle, WA, USA Rick Wilson 8 The Broad Institute, USA Keio University, Tokyo, Japan Institute of Molecular Biology (IMB), Jena, Germany Chad Nusbaum 9 The Sanger Institute, Cambridge, UK. Gesellschaft für Biotechnologische Forschung (GBF), Braunschweig, Germany Jane Rogers 10 The Sanger Institute, Cambridge, UK. Genome Therapeutics Corporation (GTC), Waltham, MA, USA Jane Rogers 11 RIKEN Human Genome Research Group, Saitama, Japan The Broad Institute, USA Todd Taylor 12 Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Steve Scherer 13 The Sanger Institute, Cambridge, UK. Jane Rogers 14 Genoscope National Sequencing Centre, Evry, France Institute for Systems Biology (ISB), Seattle, WA Washington University School of Medicine Genome Sequencing Center, St Louis, USA RIKEN Human Genome Research Group, Saitama, Japan Jean Weissenbach 15 The Broad Institute, USA Institute of Molecular Biology (IMB), Jena, Germany Institute for Systems Biology (ISB), Seattle, WA Chad Nusbaum 16 Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center, Palo Alto, CA, USA The Institute for Genomic Research (TIGR), Rockville, MD, USA The Sanger Institute, Cambridge, UK. Jeremy Schmutz 17 The Broad Institute , USA Chad Nusbaum 18 The Broad Institute, USA RIKEN Human Genome Research Group, Saitama, Japan Chad Nusbaum 19 Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center, Palo Alto, CA, USA Jeremy Schmutz 20 The Sanger Institute, Cambridge, UK. James Gilbert 21 RIKEN Human Genome Research Group, Japan Max Planck Institute for Molecular Genetics, Berlin, Germany Gesellschaft für Biotechnologische Forschung (GBF), Braunschweig, Germany Keio University School of Medicine, Tokyo, Japan Chromosome 21 Consortium Todd Taylor 22 The Sanger Institute, Cambridge, UK. The University of Oklahoma, USA. Keio University School of Medicine, Tokyo, Japan Jane Rogers X The Sanger Institute, Cambridge, UK. Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Institute of Molecular Biology (IMB), Jena, Germany Washington University School of Medicine Genome Sequencing Center, St Louis, USA Max Planck Institute for Molecular Genetics, Berlin, Germany Jane Rogers Y Washington University School of Medicine Genome Sequencing Center, St Louis, USA Rick Wilson

The UCSC Chimpanzee Genome Browser displays data from the 13 Nov. 2003 chimpanzee Arachne draft assembly (Build 1 Version 1), produced by the Chimpanzee Genome Sequencing Consortium with the following acknowledgements:

• Funding: National Human Genome Research Institute (NHGRI)
  
• Sequencing/Assembly: The sequence was assembled by teams led by Eric Lander, Ph.D., at The Broad Institute, and Richard K. Wilson, Ph.D., at the Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO, USA
  
• Alignments: LaDeana Hillier, Washington University School of Medicine, and The Broad Institute.
  
• Annotations: Washington University School of Medicine St. Louis, MO, USA, Research Group on Biomedical Informatics of IMIM/UPF (GRIB), RIKEN Genomic Sciences Center.
• UCSC Chimp Genome Browser: Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team.

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.

The UCSC Dog Genome Browser displays data from the July 2004 v. 1.0 draft assembly of the domestic dog (Canis familiaris). This assembly is provided with the following acknowledgements:

• Funding: The National Human Genome Research Institute
  
• Project Leadership: The Broad Institute, Cambridge, MA, USA
• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA - Team led by by Kerstin Lindblad-Toh, Ph.D.
• Plasmid and fosmid libraries: The Broad Institute, Cambridge, MA, USA
• BAC libraries: Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
• BAC end sequencing: Agencourt Bioscience, Beverly, MA, USA
• RH map: Centre National de la Recherche Scientifique (CNRS), France
• FISH mapping: North Carolina State University (NCSU), Raleigh, NC, USA
  
• Dog Selection: Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
• UCSC Dog Genome Browser/Initial Annotations: UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Angie Hinrichs, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin staff

The dog 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.

The UCSC Cow Genome Browser displays data from the Sep. 2004 draft assembly of the cow, version Btau_1.0 from Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC). This assembly is 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: 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.

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

• Project Oversight - Arthur Holden and Francis Collins
  
• Funding - GlaxoSmithKline, the Merck Genome Research Institute, Affymetrix, Inc., the Wellcome Trust, and six of the National Institutes, including the National Cancer Institute, the National Human Genome Research Institute, the National Institute on Deafness and Other Communication Disorders, the National Institute of Diabetes and Digestive and Kidney Disease, the National Institute of Neurological Disorders and Stroke, and the National Institute of Mental Health.
  
• Sequencing - The Broad Institute, Mass., Washington University School of Medicine in St. Louis, and the Sanger Institute in the U.K.

The remaining portion of the coverage, the map, and the assembly were produced by the Mouse Genome Sequencing Consortium, with these acknowledgements:

• Assembly - The Broad Institute's Arachne Group; Sanger Institute group: Jim Mullikin, Zemin Ning, Tim Hubbard
  
• Mapping - The Wellcome Trust Sanger Institute, the Genome Sequencing Center at Washington University School of Medicine, The Broad Institute, Mass., British Columbia Genome Sequence Centre, The Institute for Genome Research, Children's Hospital Oakland Research Institute. Mapping details can be found at http://www.ensembl.org/Mus_musculus/assembly.html.
  
• Computational Leadership for the Mouse Genome Sequencing Consortium - Ewan Birney at EBI
  
• Testing - Deanna Church at NCBI
  
• Annotations - Jackson Labs, RIKEN Genomic Sciences Center, NCBI, Ensembl, Penn State, UC Berkeley/LBNL, UCSC

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 (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420:520-562.

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:

• Project Coordination - Baylor College of Medicine Human Genome Sequencing Center, Richard Gibbs, director
  
• Funding - The National Human Genome Research Institute and the National Heart, Lung and Blood Institute of the National Institutes of Health.
  
• Sequencing - Baylor College of Medicine Human Genome Sequencing Center, Celera Genomics Group of Applera Corporation, Genome Therapeutics Corporation, The University of Utah
  
• Assembly - Baylor College of Medicine Human Genome Sequencing Center ATLAS group: Rui Chen, James Durbin, Paul Havlak
  
• Fingerprint Mapping - The British Columbia Cancer Agency Genome Sciences Center: Marco Marra, Jackie Schein
  
• BAC End Sequencing - The Institute for Genomic Research: Shaying Zhao
  
• BAC Library Construction and Distribution - Children's Hospital Oakland Research Institute: Pieter deJong
  
• Rat Genome Database - Medical College of Wisconsin

The rat sequence is freely available from the Rat Genome Project at the Baylor College of Medicine Human Genome Sequencing Center. These data are made 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 this data (the Rat 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.

The UCSC Opossum Genome Browser displays data from the Oct. 2004 draft assembly of the opossum (Monodelphis domestica). This assembly is provided with the following acknowledgements:

• Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA
  
• UCSC Opossum Genome Browser/Initial Annotations: 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.

The Feb. 2004 chicken draft sequence was produced with the following acknowledgements:

• Sequencing - The Genome Sequencing Center at Washington University School of Medicine, St. Louis.
  
• Physical Map - The Genome Sequencing Center at Washington University School of Medicine, St. Louis.
  
• 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.
  • East Lansing Map based on the RJFxlayer cross ("E" linkage maps; 56 BC animals), coordinated by Hans Cheng, Michigan State University.
  • 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, Wageningen University.
  • Chicken FPC browser: http://www.animalsciences.nl/ChickFPC/, Jan Aerts, Wageningen University.
• UCSC Chicken Genome Browser: Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik.

The G. gallus sequence is made freely available before scientific publication 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 acknowledged.
3. The Chicken analysis group is aiming to publish an initia analysis of the chicken genome sequence 2004 (submitted in the summer of 2004) which will include descriptions of the assembly, genome landscape and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson (rwilson@watson.wustl.edu), 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.

We'd like to thank the Washington University School of Medicine, St. Louis, the Chicken Mapping Consortium, and BGI for providing these data.

The 3.0 X. tropicalis draft assembly (xenTro1) was provided by the U.S. DOE Joint Genome Institute (JGI). This assembly has 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: 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.

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:
  • The Wellcome Trust Sanger Institute, UK
  • Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands
  • Max-Planck Institute for Developmental Biology, Germany
• 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:
  • Yi Zhou, Anthony DiBiase, Leonard Zon and the Zebrafish Genome Initiative at Boston Children's Hospital, Boston, MA, US - collaboration on Zebrafish WZ EST clusters, BAC End Singles/Pairs, Radiation Hybrid, and Human tBLASTn annotation tracks.
  • Washington University in St. Louis, St. Louis, MO, US - Zebrafish WZ EST clusters data
  • Ensembl, UK - Ensembl gene predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations
• UCSC Zebrafish Genome Browser: Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson (danRer2)

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.

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

• Sequencing/Assembly:
  • Genoscope, Evry, France
  • The Broad Institute,MA, USA
• Project Funding:
  • Consortium National de Recherche en Genomique, France
  • National Human Genome Research Institute (NHGRI), USA
• Initial Genome Browser Annotations:
  • Genoscope - Genscan gene predictions, GAZE gene predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - remaining annotations (based on data from Genoscope)
• UCSC Tetraodon Genome Browser: Rachel Harte, Robert Kuhn, Donna Karolchik

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).

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 JGI and the Singapore Institute of Molecular and Cell Biology (IMCB). The 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.

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.

We'd like to thank the JGI and the other members of the International Fugu Genome Consortium, including the IMCB (Singapore), the UK Human Genome Mapping Project (Hinxton), the Molecular Sciences Institute (Berkeley) and the Institute for Systems Biology (Seattle), for providing the sequence, assembly, and analysis of this genome.

The C. intestinalis v1.0 draft assembly was provided by the U.S. DOE Joint Genome Institute (JGI). This assembly has the following acknowledgements, as listed on the JGI website:

• Project Funding: Work performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.
• Project Collaborators:
  • JGI, Walnut Creek, CA, USA
  • Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
  • Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA
  • National Institute of Genetics, Mishima, Japan
  • Oak Ridge National Laboratory, Oak Ridge, TN, USA
  • Los Alamos National Laboratory, Los Alamos, NM, USA
• Annotations:
  • Colin Dewey, University of California, Berkeley, CA, USA - SNAP Gene Predictions, using the SNAP parser written by Ian Korf
  • JGI, Walnut Creek, CA, USA - JGI Gene Predictions
  • UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations
• UCSC C. intestinalis Genome Browser: Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik

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 v1.0 assembly, see the JGI Ciona web page.

The D. melanogaster data displayed in the UCSC Genome Browwser were provided by the Berkeley Drosophila Genome Project (BDGP) with the following acknowledgements:

• Sequencing and Assembly:
  • Euchromatic sequence - BDGP, Berkeley, CA, USA
  • Heterochromatic sequence - Drosophila Heterochromatin Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
• Annotations: FlyBase
• UCSC D. melanogaster (dm2) Genome Browser and additional annotations: UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA - Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik
• UCSC D. melanogaster (dm1) Genome Browser and additional annotations: UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA - Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik

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

These data were produced by the Institute for Genomic Research (TIGR). The D. ananassae Genome Browser has the following acknowledgements:

• Sequencing and Assembly: TIGR, Rockville, MD, USA, using an assembler produced by Celera
• UCSC D. ananassae 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 TIGR 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 TIGR is properly acknowledged.
3. TIGR 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.

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

• Funding: National Human Genome Research Institute (NHGRI)
• Sequencing, assembly and AGP creation: Genome Sequencing Center, WUSTL School of Medicine
• Initial Sequencing Proposal, Project Collaboration: David J. Begun and Charles H. Langley, University of California, Davis, CA, USA
• Data Downloads: Flybase
• UCSC D. yakuba Genome Browser: Angie Hinrichs, Michael Chalup and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler
• Funding: National Human Genome Research Institute (NHGRI), USA
• UCSC D. virilis Genome Browser: Angie Hinrichs, Brian Raney, Heather Trumbower, Robert Kuhn, Jennifer Jackson, 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.

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

• Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler
• Funding: National Human Genome Research Institute (NHGRI), USA
• UCSC D. mojavensis Genome Browser: Angie Hinrichs, Brian Raney, Galt Barber 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.

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 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.

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

• Funding: National Human Genome Research Institute (NHGRI) and the U.S. Department of Agriculture (USDA)
• Sequencing and assembly: BCM HGSC, Houston, TX, USA
• BAC library: Pieter de Jong and Katzutoyo Osoegawa at Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA
• UCSC A. mellifera (apiMel2)Genome Browser: Andy Pohl, Angie Hinrichs, Jennifer Jackson, and Donna Karolchik
• UCSC A. mellifera (apiMel1)Genome Browser: Angie Hinrichs, Brian Raney, Robert Kuhn, and Donna Karolchik
• Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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.

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

• Funding: National Institute of Allergy and Infectious Diseases (NIAID), French Ministry of Research, and the World Health Organization (WHO). Celera Genomics and Genoscope were funded respectively by National Institutes of Health (NIH) and French Ministry of Research.
• Project collaboration: The International Anopheles Genome Project - a collaboration between Celera Genomics, Genoscope, University of Notre Dame, EBI/Sanger Institute, EMBL, Institut Pasteur, The Institute of Molecular Biology and Biotechnology (IMBB) and The Institute for Genomic Research (TIGR).
• Sequencing and Assembly: Celera Genomics, Genoscope
• Data Downloads: Ensembl
• UCSC A. gambaie Genome Browser: Angie Hinrichs, Galt Barber and Donna Karolchik
• Initial Genome Browser Annotations: Ensembl and Celera Genomics (Ensembl Genes), the UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA (remaining annotations)

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

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.

The C. briggsae sequence was obtained from publicly available data in WormBase. This data is made available before scientific publication with the following understanding: The Genome Sequencing Center at Washington University in St. Louis and the Sanger Institute reserve the right to publish the results of any large scale analyses. If you wish to use the results of specific searches in a publication, please acknowledge these sequencing centers and check that you are using the most recent version of the sequence.

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. briggsae genome, and the WormBase consortium for providing access to the current C. briggsae sequence.

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.

The SARS draft genome assembly is based on publicly-available sequence deposited into GenBank as of 14 April 2003. Annotations showing gene predictions, locations of putative proteins, and viral mRNA and protein alignments were generated at UCSC, with the exception of the Fgenesv+ annotation contributed by Victor Solovyev of Softberry, Inc. Protein structure analysis and predictions were determined by using the Sequence Alignment and Modeling (SAM) T02 tool.

The NISC sequence data were compiled from existing GenBank records. In addition to long-range assembly and standard feature annotation, the results of several analyses are available, including pair-wise sequence alignments, intrinsic sequence properties, and sequence comparisons that reveal regions highly conserved across multiple species. Flat files of the assembled sequence and annotations can be obtained from http://www.nisc.nih.gov/data/.

These data are made available for public use with specific data release and use restrictions.

We'd like to thank the NISC Comparative Sequencing Program team for providing the data and comparative analyses for this Genome Browser release. Special thanks go to Elliott Margulies at NHGRI for serving as the main liaison between NHGRI and UCSC and for contributing several annotation tracks to the browser.

• Affymetrix (David Kulp, Alan Williams, Ray Wheeler, Greg Helt, Tom Gingeras, Guoying Liu, Andy Kimbrough, Hajime Matsuzaki, Rui Mei, Keith Jones): Development of genotyping array and genotype data for Affymetrix 120K SNP annotation track, Affymetrix transcriptome data for chr 21 and 22, Genie gene prediction track, design and analysis support in the early stages of the UCSC Human Genome project, including software for the synthetic chromosome 22 data we used to test our assembly methods.
• BAC Resource Consortium: Cytogenetic markers (FISH-mapped clones annotation track).
• Baylor College of Medicine (Richard Gibbs, John Bouck, Kim Worley and James Durbin): Rat Genome sequence data, D. pseudoobscura sequence for alignment tracks with D. melanogaster genome.
• Berkeley Drosophila Genome Project (BDGP): Data for D. melanogaster gene annotations.
• Bioinformatics Solutions, Inc. (Ming Li and colleagues): Pattern Hunter mouse homology track.
• Case Western Reserve University (Evan Eichler and Jeff Bailey): Segmental duplications annotation track.
• Cedars-Sinai Medical Center (CSMC): FISH-mapped clones annotation track.
• CNRS Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France (Michel Weber): miRNA Data annotation track (in collaboration with Sam Griffiths-Jones of The Wellcome Trust Sanger Institute).
• Cold Spring Harbor Laboratory
  --(Lincoln Stein): HapMap data.
  --(Ivo Grosse and Michael Q. Zhang): Predictions for First Exon Finder annotation track.
• Ensembl (Ewan Birney, Guy Slater, Imre Vastrik, Arek Kasprzyk, Michele Clamp): Ensembl Gene predictions annotation track, data exchange formats, TPF clone map coordination, exonerate mouse homology track, early help placing FISH-mapped clones.
• EMBL (Peter Bork): Mouse pseudogene predictions used for Bork Pseudogenes custom annotation track.
• FlyBase: Curated Drosophila gene annotations.
• Fred Hutchison Cancer Research Center (FHCRC) (Barbara Trask): FISH-mapped clones annotation track.
• Gene Ontology (GO) Consortium: Structured annotations for Gene Sorter.
• Genetic Information Research Institute: Repbase, repeatmasking.
• Genome Informatics Research Lab (GIRL) within Grup de Recerca en Informàtica Mèdica (GRIB) (Francisco Câmara Ferreira, Roderic Guigó): Geneid and SGP gene prediction annotation tracks.
• Genomics Institute of the Novartis Research Foundation (GNF): Expression data using Affymetrix chips for GNF Expression Atlas annotation tracks.
• Genoscope (Jean Weissenbach and Olivier Jaillon): Exofish program, Tetraodon nigroviridis sequence for Tetraodon Blat alignments annotation tracks, data for Anopheles Evolutionary Conserved Regions annotation track.
• The Institute for Genomic Research (TIGR): TIGR Gene Index annotation track.
• Institute for Systems Biology (Arian Smit): RepeatMasker repeat identification and masking software and libraries.
• The Jackson Laboratory (Carol Bult): Mouse ortholog links from known genes track.
• Kyoto University, GenomeNet: Kyoto Encyclopedia of Genes and Genomes (KEGG) - pathway diagrams for Known Genes annotation track.
• Los Alamos National Laboratory (LANL): FISH-mapped clones annotation track.
• Mammalian Gene Collection (MGC) Project: Data used in MGC Genes annotation track.
• Massachusetts Institute of Technology (MIT) (Chris Burge): Genscan gene prediction program.
• Medical Research Council Laboratory of Molecular Biology (Julian Gough - now at Stanford School of Medicine): Superfamily database.
• Mount Sinai School of Medicine (Gary Benson): Tandem Repeats Finder.
• National Cancer Institute (NCI): The Cancer Genome Anatomy Project (CGAP) - FISH-mapped clones annotation track. SAGE project (in collaboration with NCBI).
• National Center for Biotechnology Information (NCBI)
  --(Deanna Church): Mouse synteny track, database of whole genome shotgun mouse reads and assemblies used for mouse tracks.
  --(Greg Schuler): GenBank freezes of human clones used in the assembly, NT contigs of multiple finished clones, STS maps (in earlier freezes), specially-formatted versions of the finished chromosomes.
  --(Steve Sherry): SNP tracks.
  --(Wonhee Jang): FISH-mapped clones annotation track.
  --(Danielle and Jean Thierry-Mieg): Acembly Genes annotation track.
  --(Lukas Wagner): 3' EST track in the July 2000 browser.
  --dbSNP database.
  --(Kim Pruitt, Donna Maglott): RefSeq and Entrez Gene databases.
  --Serial Analysis of Gene Expression Tag to Gene Mapping (SAGEmap) data resource.
• National Human Genome Research Institute (NHGRI)
  --(Elliott Margulies, Pamela Jacques Thomas, Eric Green): Collaboration and annotations for NISC browser, including curated gene annotations, DNAse I Hypersensitive Sites annotation, Multi-species Conserved Sequences (MCS) tracks, Binomial_25 Conservation Scores, ZooSeq Blastz alignments tracks.
  --Data for ENCyclopedia Of DNA Elements (ENCODE) annotation track.
• Ohio State University Bioinformatics & Computational Biology Group (Ramana V. Davuluri): Predictions for First Exon Finder annotation track.
• Pennsylvania State University Bioinformatics Group (Scott Schwartz, Webb Miller, Zheng Zhang, Ross Hardison, Francesca Chiaromonte, Laura Elnitski): Blastz alignment program, multiz alignment protram, Genome Alignment and Annotation Database (GALA), collaboration on multiple alignment annotation tracks, ENCODE annotation tracks.
• Perlegen Sciences (David Hinds, Kelly Frazer, and David Cox): STS markers for the Haplotype Blocks annotation track on chr 21, SNP data for the Affymetrix 120K SNP track, TNG radiation hybrid map.
• RIKEN Genomic Sciences Center: Chimpanzee BAC end sequence data, mouse annotations, human genome sequence contributions.
• Roswell Park Cancer Institute (RPCI): FISH-mapped clones annotation track.
• SNP Consortium: Data for SNP annotation tracks.
• Softberry Inc. (Victor Solovyev): Fgenesh++ and Fgenesv+ gene predictions, TSSW promoters tracks.
• Sperling Biomedical Foundation (Thomas Pringle): Technical consultant on Proteome Browser, avid Genome Browser user and the source of a myriad of ideas for expanding its functionality, early assistance and support with user's guides, email moderation, web links, and testing.
• Stanford University School of Medicine (Richard Myers Lab): Data set for Human Promoters custom annotation track.
• Swiss-Prot: Protein data and human curated annotation from the Swiss-Prot protein knowledgebase, TrEMBL, and TrEMBL-NEW.
• Universidad de Granada, Grupo de Bioinformática, Spain (Jose L. Oliver): Isochore custom annotation track.
• University of CA, Berkeley (Lior Pachter, Simon Cawley, Marina Alexandersson): SLAM Gene prediction annotation tracks.
• University of CA, San Francisco Cancer Center: FISH-mapped clones annotation track.
• University of Pennsylvania (Y. Thomas Gan): Database of Transcribed Sequences (DoTS) Genes custom annotation track.
• University of Vienna, Institute for Theoretical Chemistry and Structural Biology, Theoretical Biochemistry Group: Vienna RNA utility RNAplot - Known Genes annotation track.
• Washington University in St. Louis
  --(Robert Waterston (now at UW), John McPhearson, Asif Chinwalla, Shiaw-Pyng Yang, John Wallis and LaDeana Hillier): Fingerprint-based map of BAC clones from the human genome and a corresponding layout of sequenced clones, plasmid end reads, BACend analysis, CpG islands.
  --(Sean Eddy and Todd Lowe (now at UCSC)): RNA Genes track.
  --(Michael Brent's Computational Genomics Group): Twinscan Gene prediction annotation track.
• Wellcome Trust Sanger Institute
  --(Jennifer Ashurst, James Gilbert, John Sulston, Jane Rogers, Jim Mullikin, Richard Durbin, Steve Searle, Ian Dunham and the annotation teams): Vega Genes and Pseudogenes, Sanger 20 and Sanger 22 Genes and Pseudogenes. Plasmid end reads, processing of whole genome shotgun mouse reads.
  --(Sam Griffiths-Jones): miRNA Data annotation track (in collaboration with Michel Weber of CNRS Université Paul Sabatier).
  --Protein Families Database of Alignments and HMMs (Pfam).
• The Broad Institute (Eric Lander, Mike Zody, Chad Nusbaum): Plasmid end reads. Human working draft sequence analysis project. Special thanks to Eric for inviting us to join the Hardcore Analysis Group for the draft sequence project and for his direction of that group.
• WormBase (Lincoln Stein): Wormbase curated gene annotations for C. elegans genome.

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.