Methods for automated genome-scale metabolic model reconstruction

Faria, José P.; Rocha, Miguel; Rocha, Isabel; Henry, Christopher S.

doi:10.1042/BST20170246

Title: Methods for automated genome-scale metabolic model reconstruction

Journal Article · Tue Jul 31 00:00:00 EDT 2018 · Biochemical Society Transactions

DOI:https://doi.org/10.1042/BST20170246· OSTI ID:1493924

Faria, José P. ^[1]; Rocha, Miguel ^[2]; Rocha, Isabel ^[2]; Henry, Christopher S. ^[1]

Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
Univ. of Minho, Braga (Portugal). Centre of Biological Engineering

In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. We are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1493924

Journal Information:: Biochemical Society Transactions, Vol. 46, Issue 4; ISSN 0300-5127

Publisher:: Portland PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 29 works

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