About the Authors

Shibu Yooseph

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

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

Granger Sutton

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

Douglas B Rusch

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

Aaron L Halpern

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

Shannon J Williamson

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

Karin Remington

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

Jonathan A Eisen

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

Karla B Heidelberg

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

Gerard Manning

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

Weizhong Li

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

Lukasz Jaroszewski

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

Piotr Cieplak

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

Christopher S Miller

Affiliation University of California Los Angeles

Huiying Li

Affiliation University of California Los Angeles

Susan T Mashiyama

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

Marcin P Joachimiak

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

Christopher van Belle

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

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

David A Soergel

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

Yufeng Zhai

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

Kannan Natarajan

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

Shaun Lee

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

Benjamin J Raphael

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

Vineet Bafna

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

Robert Friedman

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

Steven E Brenner

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

Adam Godzik

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

David Eisenberg

Affiliation University of California Los Angeles

Jack E Dixon

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

Susan S Taylor

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

Robert L Strausberg

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

Marvin Frazier

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

J. Craig Venter

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

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.