title: Deriving enzymatic and taxonomic signatures of metagenomes from short read data.
abstract: BACKGROUND
  We propose a method for deriving enzymatic signatures from short read metagenomic data of unknown species. The short read data are converted to six pseudo-peptide candidates. We search for occurrences of Specific Peptides (SPs) on the latter. SPs are peptides that are indicative of enzymatic function as defined by the Enzyme Commission (EC) nomenclature. The number of SP hits on an ensemble of short reads is counted and then converted to estimates of numbers of enzymatic genes associated with different EC categories in the studied metagenome. Relative amounts of different EC categories define the enzymatic spectrum, without the need to perform genomic assemblies of short reads.
  
  
  RESULTS
  The method is developed and tested on 22 bacteria for which there exist many EC annotations in Uniprot. Enzymatic signatures are derived for 3 metagenomes, and their functional profiles are explored.We extend the SP methodology to taxon-specific SPs (TSPs), allowing us to estimate taxonomic features of metagenomic data from short reads. Using recent Swiss-Prot data we obtain TSPs for different phyla of bacteria, and different classes of proteobacteria. These allow us to analyze the major taxonomic content of 4 different metagenomic data-sets.
  
  
  CONCLUSIONS
  The SP methodology can be successfully extended to applications on short read genomic and metagenomic data. This leads to direct derivation of enzymatic signatures from raw short reads. Furthermore, by employing TSPs, one obtains valuable taxonomic information.
authors.affiliation: School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Uri
authors.initials: U
authors.lastname: Weingart
authors.forename: Erez
authors.initials: E
authors.lastname: Persi
authors.forename: Uri
authors.initials: U
authors.lastname: Gophna
authors.forename: David
authors.initials: D
authors.lastname: Horn
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D001426:Bacterial Proteins / Q000032:analysis; D030562:Databases, Protein; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D016680:Genome, Bacterial; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D010455:Peptides / Q000032:analysis
chemical_list: D001426:Bacterial Proteins; D010455:Peptides