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Research Article

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

  • Alexis P. Yelton,

    Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America

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  • Brian C. Thomas,

    Affiliation: Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America

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  • Sheri L. Simmons,

    Affiliation: Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America

    Current address: Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America.

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  • Paul Wilmes,

    Affiliation: Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America

    Current address: Department of Environment and Agro-Biotechnologies, Centre de Recherche Public – Gabriel Lippmann, Belvaux, Grand-Duchy of Luxembourg.

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  • Adam Zemla,

    Affiliation: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America

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  • Michael P. Thelen,

    Affiliation: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America

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  • Nicholas Justice,

    Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America

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  • Jillian F. Banfield mail

    jbanfield@berkeley.edu

    Affiliations: Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America, Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America

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  • Published: October 20, 2011
  • DOI: 10.1371/journal.pcbi.1002230

About the Authors

Alexis P. Yelton, Brian C. Thomas, Jillian F. Banfield
Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
Sheri L. Simmons, Paul Wilmes, Jillian F. Banfield
Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
Adam Zemla, Michael P. Thelen
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
Nicholas Justice
Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America

Corresponding Author

Email: jbanfield@berkeley.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: APY JFB. Performed the experiments: APY BCT SLS PW AZ MPT NJ. Analyzed the data: APY. Contributed reagents/materials/analysis tools: BCT. Wrote the paper: APY BCT JFB.