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MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

Kishori M Konwar1, Niels W Hanson2, Antoine P Pagé1 and Steven J Hallam12*

Author Affiliations

1 Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada

2 Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC Canada

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BMC Bioinformatics 2013, 14:202  doi:10.1186/1471-2105-14-202

Published: 21 June 2013

Abstract

Background

A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information. The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems.

Results

Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. The pipeline accepts assembled or unassembled nucleotide sequences, performs quality assessment and control, predicts and annotates noncoding genes and open reading frames, and produces inputs to PathoLogic. In addition to constructing ePGDBs, MetaPathways uses MLTreeMap to build phylogenetic trees for selected taxonomic anchor and functional gene markers, converts General Feature Format (GFF) files into concatenated GenBank files for ePGDB construction based on third-party annotations, and generates useful file formats including Sequin files for direct GenBank submission and gene feature tables summarizing annotations, MLTreeMap trees, and ePGDB pathway coverage summaries for statistical comparisons.

Conclusions

MetaPathways provides users with a modular annotation and analysis pipeline for predicting metabolic interaction networks from environmental sequence information using an alternative to KEGG pathways and SEED subsystems mapping. It is extensible to genomic and transcriptomic datasets from a wide range of sequencing platforms, and generates useful data products for microbial community structure and function analysis. The MetaPathways software package, installation instructions, and example data can be obtained from http://hallam.microbiology.ubc.ca/MetaPathways webcite.

Keywords:
Environmental pathway/Genome Database (ePGDB); Metagenome; Pathway tools; PathoLogic; MetaCyc; Microbial community; Metabolism; Metabolic interaction networks