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Open Access Methodology article

Deriving enzymatic and taxonomic signatures of metagenomes from short read data

Uri Weingart1, Erez Persi1, Uri Gophna2 and David Horn1*

Author Affiliations

1 School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel

2 Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel

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BMC Bioinformatics 2010, 11:390  doi:10.1186/1471-2105-11-390

Published: 22 July 2010

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.