Deriving enzymatic and taxonomic signatures of metagenomes from short read data

BMC Bioinformatics

Methodology Article

Uri Gophna¹  David Horn²  Erez Persi²  Uri Weingart² 

[1] Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Tel Aviv, Israel;School of Physics and Astronomy, Tel Aviv University, 69978, Tel Aviv, Israel;

关键词: Enzyme Commission;    Short Read;    Aminoacyl tRNA Synthetase;    Taxonomic Analysis;    Metagenomic Data;   

DOI  :  10.1186/1471-2105-11-390

 received in 2010-03-03, accepted in 2010-07-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundWe 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.ResultsThe 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Weingart et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.