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Research Article

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

  • Florent E. Angly mail,

    forent.angly@gmail.com

    Affiliations: Biology Department, San Diego State University, San Diego, California, United States of America, Computational Science Research Center, San Diego State University, San Diego, California, United States of America

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  • Dana Willner,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Alejandra Prieto-Davó,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Robert A. Edwards,

    Affiliations: Biology Department, San Diego State University, San Diego, California, United States of America, Computer Science Department, San Diego State University, San Diego, California, United States of America, Mathematics and Computer Science Division, Argonne National Lab, Argonne, Illinois, United States of America

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  • Robert Schmieder,

    Affiliations: Computational Science Research Center, San Diego State University, San Diego, California, United States of America, Computer Science Department, San Diego State University, San Diego, California, United States of America

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  • Rebecca Vega-Thurber,

    Affiliation: Biology Department, Florida International University, Miami, Florida, United States of America

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  • Dionysios A. Antonopoulos,

    Affiliation: Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Katie Barott,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Matthew T. Cottrell,

    Affiliation: School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America

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  • Christelle Desnues,

    Affiliation: URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Université de la Méditerranée, Marseille, France

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  • Elizabeth A. Dinsdale,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Mike Furlan,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Matthew Haynes,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Matthew R. Henn,

    Affiliation: The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America

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  • Yongfei Hu,

    Affiliation: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

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  • David L. Kirchman,

    Affiliation: School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America

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  • Tracey McDole,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • John D. McPherson,

    Affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada

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  • Folker Meyer,

    Affiliation: Mathematics and Computer Science Division, Argonne National Lab, Argonne, Illinois, United States of America

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  • R. Michael Miller,

    Affiliation: Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America

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  • Egbert Mundt,

    Affiliation: Poultry Diagnostic and Research Center, College of Veterinary Medicine, The University of Georgia, Athens, Georgia, United States of America

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  • Robert K. Naviaux,

    Affiliation: School of Medicine, University of California San Diego, San Diego, United States of America

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  • Beltran Rodriguez-Mueller,

    Affiliations: Biology Department, San Diego State University, San Diego, California, United States of America, Computational Science Research Center, San Diego State University, San Diego, California, United States of America

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  • Rick Stevens,

    Affiliation: Mathematics and Computer Science Division, Argonne National Lab, Argonne, Illinois, United States of America

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  • Linda Wegley,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Lixin Zhang,

    Affiliation: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

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  • Baoli Zhu,

    Affiliation: CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

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  • Forest Rohwer

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Published: December 11, 2009
  • DOI: 10.1371/journal.pcbi.1000593

About the Authors

Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Katie Barott, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Tracey McDole, Beltran Rodriguez-Mueller, Linda Wegley, Forest Rohwer
Biology Department, San Diego State University, San Diego, California, United States of America
Florent E. Angly, Robert Schmieder, Beltran Rodriguez-Mueller
Computational Science Research Center, San Diego State University, San Diego, California, United States of America
Robert A. Edwards, Robert Schmieder
Computer Science Department, San Diego State University, San Diego, California, United States of America
Robert A. Edwards, Folker Meyer, Rick Stevens
Mathematics and Computer Science Division, Argonne National Lab, Argonne, Illinois, United States of America
Dionysios A. Antonopoulos, R. Michael Miller
Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
Rebecca Vega-Thurber
Biology Department, Florida International University, Miami, Florida, United States of America
Matthew T. Cottrell, David L. Kirchman
School of Marine Science and Policy, University of Delaware, Lewes, Delaware, United States of America
Christelle Desnues
URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Université de la Méditerranée, Marseille, France
Matthew R. Henn
The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
Yongfei Hu, Lixin Zhang, Baoli Zhu
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
John D. McPherson
Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
Egbert Mundt
Poultry Diagnostic and Research Center, College of Veterinary Medicine, The University of Georgia, Athens, Georgia, United States of America
Robert K. Naviaux
School of Medicine, University of California San Diego, San Diego, United States of America

Corresponding Author

Email: forent.angly@gmail.com

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: FEA RS RVT FR. Performed the experiments: FEA. Analyzed the data: FEA DW. Contributed reagents/materials/analysis tools: FEA RAE. Wrote the paper: FEA DW APD. Collected samples and prepared metagenome: DAA KB MTC CD EAD MF MH MRH YH DLK TM JDM FM RMM EM RKN BRM RS LW LZ BZ.