Deriving enzymatic and taxonomic signatures of metagenomes from short read data

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 taxonomi...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Uri Weingart, Erez Persi, Uri Gophna, David Horn
• Keywords: BMCBI 2010, Enzymatic, Enzymatic Signatures, Short Reads