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  UCSC Genome Browser Acknowledgments

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

CGWB ( Cancer Genome Workbench) uses the UCSC browser code. Please check USCS browswer for up to date links to view the contributions of the UCSC Genome Browser project team. Special thanks for their efforts !!!



  Human Genome: Acknowledgements
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HHMI CISI
NHGRI

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.



  Human Genome: Data Sources

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

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

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



  Chimpanzee Genome

The UCSC Chimpanzee Genome 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:

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.



  Dog Genome

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:

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 of MIT and Harvard, 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.



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

The remaining portion of the coverage, the map, and the assembly were 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 (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420:520-562.



  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 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.



  Chicken Genome

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

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.



  X. tropicalis Genome

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.



  Zebrafish Genome

The Zv3 Zebrafish draft assembly (danRer1) was provided by The Wellcome Trust Sanger Institute. This assembly has the following acknowledgements:

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 Zv3 assembly, see the Sanger Institute's Danio rerio Sequencing Project web page.



  Tetraodon Genome

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

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

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


  Fugu Genome

The Fugu whole genome shotgun assembly was provided by the U.S. DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium, led by 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.



  C. Intestinalis 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:

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.



  D. melanogaster Genome

This data was provided by the Berkeley Drosophila Genome Project (BDGP). We'd like to thank the BDGP and the Flybase Consortium for providing the sequence, assembly, and analysis of this genome. The FlyBase Consortium includes Drosophila researchers and computer scientists at Harvard University, University of Cambridge, Indiana University, the University of California, Berkeley and the European Bioinformatics Institute (EBI).



  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:

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



  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.


  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.



  C. briggsae Genome

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.



  Yeast Genome

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 at MIT/Harvard for providing the data and annotations for this release.



  SARS Genome

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.



  NISC Comparative Sequencing Program

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.



  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.