title: Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
abstract: BACKGROUND
  Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases.
  
  
  RESULTS
  We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure.
  
  
  BACKGROUND
  http://gobics.de/TaxyPro.
  
  
  BACKGROUND
  Supplementary Material is available at Bioinformatics online.
authors: Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
authors: Heiner
authors: H
authors: Klingenberg
authors: Kathrin Petra
authors: KP
authors: Aßhauer
authors: Thomas
authors: T
authors: Lingner
authors: Peter
authors: P
authors: Meinicke
mesh_terms: D019641:DNA, Archaeal / Q000032:analysis; D004279:DNA, Viral / Q000032:analysis; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny; D017434:Protein Structure, Tertiary
chemical_list: D019641:DNA, Archaeal; D004279:DNA, Viral