Deriving enzymatic and taxonomic signatures of metagenomes from short read data

Uri Weingart, Erez Persi, Uri Gophna, David Horn*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number390
JournalBMC Bioinformatics
StatePublished - 22 Jul 2010


FundersFunder number
Edmond J. Safra Bioinformatics
McDonnel foundation
Ministerio de Sanidad, Consumo y Bienestar Social
United States-Israel Binational Science Foundation


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