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Research Article

Fast Statistical Alignment

  • Robert K. Bradley mail,

    rbradley@berkeley.edu

    Affiliations: Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America, Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America

    X
  • Adam Roberts,

    Affiliation: Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America

    X
  • Michael Smoot,

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

    X
  • Sudeep Juvekar,

    Affiliation: Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America

    X
  • Jaeyoung Do,

    Affiliation: Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America

    X
  • Colin Dewey,

    Affiliations: Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America, Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America

    X
  • Ian Holmes,

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

    X
  • Lior Pachter

    Affiliations: Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America, Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America

    X
  • Published: May 29, 2009
  • DOI: 10.1371/journal.pcbi.1000392

About the Authors

Robert K. Bradley, Lior Pachter
Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
Robert K. Bradley, Lior Pachter
Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, California, United States of America
Adam Roberts, Sudeep Juvekar
Department of Electrical Engineering & Computer Science, University of California Berkeley, Berkeley, California, United States of America
Michael Smoot
Department of Bioengineering, University of California San Diego, San Diego, California, United States of America
Jaeyoung Do, Colin Dewey
Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
Colin Dewey
Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America
Ian Holmes
Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America

Corresponding Author

Email: rbradley@berkeley.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Wrote the paper: RKB CD LP. Led the development of FSA, wrote most of the code base, and developed the query-specific learning method: RKB. Redesigned the sequence annealing algorithm, constituted the core development team, and managed the project: RKB CD LP. Developed the GUI: AR. Developed a preliminary version of the GUI: MS. Developed the iterative refinement technique: SJ. Developed the parellelization and database modes: JD CD. Provided advice on the dart library, including its algorithms, programming and software components: IH. Created the FSA webserver: LP.