title: Real time metagenomics: using k-mers to annotate metagenomes.
abstract: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA. redwards@mail.sdsu.edu
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.forename: Terry
authors.initials: T
authors.lastname: Disz
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
mesh_terms: D000465:Algorithms; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA