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

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.