Degradation Network Reconstruction Guided by Metagenomic Data

Rafael Bargiela; Manuel Ferrer

doi:10.1007/978-1-4939-6691-2_9

Degradation Network Reconstruction Guided by Metagenomic Data

Methods Mol Biol. 2017:1539:145-157. doi: 10.1007/978-1-4939-6691-2_9.

Authors

Rafael Bargiela¹, Manuel Ferrer²

Affiliations

¹ Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain.
² Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain. mferrer@icp.csic.es.

PMID: 27900688
DOI: 10.1007/978-1-4939-6691-2_9

Abstract

Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.

Keywords: AromaDeg; Aromatics; Biodegradation; Metagenomics; Network reconstruction; Next-generation sequencing; Pathways; Pollutants.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biodegradation, Environmental*
Computational Biology / methods*
High-Throughput Nucleotide Sequencing
Metabolic Networks and Pathways / genetics
Metagenome*
Metagenomics* / methods
Software