title: PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.
abstract: The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based function assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). This new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.
authors.affiliation: Computation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Davis
authors.affiliation: Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA; Fellowship for Interpretation of GenomesBurr Ridge, IL, USA.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.affiliation: Department of Microbiology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.affiliation: Computation Institute, University of ChicagoChicago, IL, USA; Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.affiliation: Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA; Fellowship for Interpretation of GenomesBurr Ridge, IL, USA.
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.affiliation: Computation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA.
authors.forename: Maulik
authors.initials: M
authors.lastname: Shukla
authors.affiliation: Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA; Fellowship for Interpretation of GenomesBurr Ridge, IL, USA.
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech University Blacksburg, VA, USA.
authors.forename: Alice R
authors.initials: AR
authors.lastname: Wattam
authors.affiliation: Computation Institute, University of ChicagoChicago, IL, USA; Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne IL, USA.
authors.forename: Hyunseung
authors.initials: H
authors.lastname: Yoo
keywords: FIGfams; RAST; comparative genomics; genome annotation; metabolic modeling