Advertisement
Research Article

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

  • Shibu Yooseph mail,

    To whom correspondence should be addressed. E-mail: Shibu.Yooseph@venterinstitute.org

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Granger Sutton,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Douglas B Rusch,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Aaron L Halpern,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Shannon J Williamson,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Karin Remington,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Jonathan A Eisen,

    Affiliations: J. Craig Venter Institute, Rockville, Maryland, United States of America, University of California, Davis, California, United States of America

    X
  • Karla B Heidelberg,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Gerard Manning,

    Affiliation: Razavi-Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America

    X
  • Weizhong Li,

    Affiliation: Burnham Institute for Medical Research, La Jolla, California, United States of America

    X
  • Lukasz Jaroszewski,

    Affiliation: Burnham Institute for Medical Research, La Jolla, California, United States of America

    X
  • Piotr Cieplak,

    Affiliation: Burnham Institute for Medical Research, La Jolla, California, United States of America

    X
  • Christopher S Miller,

    Affiliation: University of California Los Angeles

    X
  • Huiying Li,

    Affiliation: University of California Los Angeles

    X
  • Susan T Mashiyama,

    Affiliation: University of California Berkeley, Berkeley, California, United States of America

    X
  • Marcin P Joachimiak,

    Affiliation: University of California Berkeley, Berkeley, California, United States of America

    X
  • Christopher van Belle,

    Affiliation: University of California Berkeley, Berkeley, California, United States of America

    X
  • John-Marc Chandonia,

    Affiliations: University of California Berkeley, Berkeley, California, United States of America, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America

    X
  • David A Soergel,

    Affiliation: University of California Berkeley, Berkeley, California, United States of America

    X
  • Yufeng Zhai,

    Affiliation: Razavi-Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America

    X
  • Kannan Natarajan,

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

    X
  • Shaun Lee,

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

    X
  • Benjamin J Raphael,

    Affiliation: Brown University, Providence, Rhode Island, United States of America

    X
  • Vineet Bafna,

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

    X
  • Robert Friedman,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Steven E Brenner,

    Affiliation: University of California Berkeley, Berkeley, California, United States of America

    X
  • Adam Godzik,

    Affiliation: Burnham Institute for Medical Research, La Jolla, California, United States of America

    X
  • David Eisenberg,

    Affiliation: University of California Los Angeles

    X
  • Jack E Dixon,

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

    X
  • Susan S Taylor,

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

    X
  • Robert L Strausberg,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Marvin Frazier,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • J. Craig Venter

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Published: March 13, 2007
  • DOI: 10.1371/journal.pbio.0050016
  • Published in PLOS Biology

About the Authors

Shibu Yooseph, Granger Sutton, Douglas B Rusch, Aaron L Halpern, Shannon J Williamson, Karin Remington, Jonathan A Eisen, Karla B Heidelberg, Robert Friedman, Robert L Strausberg, Marvin Frazier, J. Craig Venter
J. Craig Venter Institute, Rockville, Maryland, United States of America
Jonathan A Eisen
University of California, Davis, California, United States of America
Gerard Manning, Yufeng Zhai
Razavi-Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America
Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Adam Godzik
Burnham Institute for Medical Research, La Jolla, California, United States of America
Christopher S Miller, Huiying Li, David Eisenberg
University of California Los Angeles
Susan T Mashiyama, Marcin P Joachimiak, Christopher van Belle, John-Marc Chandonia, David A Soergel, Steven E Brenner
University of California Berkeley, Berkeley, California, United States of America
John-Marc Chandonia
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
Kannan Natarajan, Shaun Lee, Vineet Bafna, Jack E Dixon, Susan S Taylor
University of California San Diego, San Diego, California, United States of America
Benjamin J Raphael
Brown University, Providence, Rhode Island, United States of America

Corresponding Author

Email: Shibu.Yooseph@venterinstitute.org

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

SY contributed to the design and implementation of the clustering process, and the subsequent analyses of the clusters; he also contributed to and coordinated all of the analyses in the paper, and wrote a large portion of the paper. GS contributed to the design and analysis of the clustering process, contributed ideas, analysis, and also wrote parts of the paper. DBR identified ORFs from the assemblies, performed the all-against-all BLAST searches, contributed to GOS kingdom assignment, and contributed analysis tools and ideas. ALH performed the assembly of GOS sequences, and contributed analysis tools and ideas. SW contributed to the analysis of viral sequences. KR contributed to project planning and paper writing. JAE performed the analysis of UV damage repair enzymes, and also contributed to paper writing. KBH, RF, and RLS contributed to project planning. GM performed the profile HMM searches, carried out the domain analysis, and contributed to paper writing. WL and AG carried out the ORFan analysis and contributed to paper writing. LJ contributed to the profile-profile search process. PC and AG carried out the analysis of proteases and contributed to paper writing. CSM, HL, and DE carried out the analysis of novel clusters, the analysis of metabolic enzymes and contributed to paper writing. YZ contributed to the profile HMM searches and domain analysis. STM, MPJ, CvB, DAS, and SEB carried out the analysis of Pfam domain distributions in GOS and current proteins, analysis of IDO, contributed to GOS kingdom assignment, and also contributed to paper writing. DAS and SEB also contributed to the Ka/Ks test. JMC and SEB carried out the analysis on the implications for structural genomics and contributed to paper writing. SL, KN, SST, and JED carried out the phosphatase analysis and contributed to paper writing. SST and JED also contributed to project planning. BJR and VB contributed to the analysis of cluster size distribution, family discovery rate, and contributed to paper writing. MF contributed to paper writing, project planning, and ideas for analysis. JCV conceived and coordinated the project, and supplied ideas.