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Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002; 12:1611-8. [PMID: 12368254 PMCID: PMC187536 DOI: 10.1101/gr.361602] [Citation(s) in RCA: 1168] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
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Affiliation(s)
- Jason E. Stajich
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - David Block
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Kris Boulez
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Steven E. Brenner
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Stephen A. Chervitz
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Chris Dagdigian
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Georg Fuellen
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - James G.R. Gilbert
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Ian Korf
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Hilmar Lapp
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Heikki Lehväslaiho
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Chad Matsalla
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Chris J. Mungall
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Brian I. Osborne
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Matthew R. Pocock
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Peter Schattner
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Martin Senger
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Lincoln D. Stein
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Elia Stupka
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Mark D. Wilkinson
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
| | - Ewan Birney
- University Program in Genetics, Duke University, Durham, North Carolina 27710, USA; National Research Council of Canada, Plant Biotechnology Institute, Saskatoon, SK S7N OW9 Canada; AlgoNomics, B 9052 Gent, Belgium; Department of Plant and Molecular Biology, University of California, Berkeley, California 94720, USA; Affymetrix, Inc., Emeryville, California 94608, USA; Open Bioinformatics Foundation, Somerville, Massachusetts 02144, USA; Integrated Functional Genomics, IZKF, University Hospital Muenster, 48149 Muenster, Germany; The Welcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK; Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA; Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, USA; European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK; Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon SK, S7N 0X2 Canada; Berkeley Drosophila Genome Project, University of California, Berkeley, California 94720, USA; Cogina, New York City, New York 10022, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Institute of Molecular and Cell Biology, 117609 Singapore
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