title: MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.
abstract: BACKGROUND
  Metagenomes provide access to the taxonomic composition and functional capabilities of microbial communities. Although metagenomic analysis methods exist for estimating overall community composition or metabolic potential, identifying specific taxa that encode specific functions or pathways of interest can be more challenging. Here we present MetAnnotate, which addresses the common question: "which organisms perform my function of interest within my metagenome(s) of interest?" MetAnnotate uses profile hidden Markov models to analyze shotgun metagenomes for genes and pathways of interest, classifies retrieved sequences either through a phylogenetic placement or best hit approach, and enables comparison of these profiles between metagenomes.
  
  
  RESULTS
  Based on a simulated metagenome dataset, the tool achieves high taxonomic classification accuracy for a broad range of genes, including both markers of community abundance and specific biological pathways. Lastly, we demonstrate MetAnnotate by analyzing for cobalamin (vitamin B12) synthesis genes across hundreds of aquatic metagenomes in a fraction of the time required by the commonly used Basic Local Alignment Search Tool top hit approach.
  
  
  CONCLUSIONS
  MetAnnotate is multi-threaded and installable as a local web application or command-line tool on Linux systems. Metannotate is a useful framework for general and/or function-specific taxonomic profiling and comparison of metagenomes.
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.
authors.forename: Pavel
authors.initials: P
authors.lastname: Petrenko
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.
authors.forename: Briallen
authors.initials: B
authors.lastname: Lobb
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Kurtz
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.
authors.forename: Josh D
authors.initials: JD
authors.lastname: Neufeld
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada. acdoxey@uwaterloo.ca.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Doxey
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D002965:Classification; D054892:Metagenome; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software; D014805:Vitamin B 12 / Q000235:genetics* / Q000378:metabolism
chemical_list: D014805:Vitamin B 12