Methods for automated genome-scale metabolic model reconstruction
Abstract
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.
- Authors:
-
- Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
- Univ. of Minho, Braga (Portugal). Centre of Biological Engineering
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1493924
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biochemical Society Transactions
- Additional Journal Information:
- Journal Volume: 46; Journal Issue: 4; Journal ID: ISSN 0300-5127
- Publisher:
- Portland Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; genome annotation; genome-scale metabolic model; metabolic network
Citation Formats
Faria, José P., Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S.. Methods for automated genome-scale metabolic model reconstruction. United States: N. p., 2018.
Web. doi:10.1042/BST20170246.
Faria, José P., Rocha, Miguel, Rocha, Isabel, & Henry, Christopher S.. Methods for automated genome-scale metabolic model reconstruction. United States. https://doi.org/10.1042/BST20170246
Faria, José P., Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S.. Tue .
"Methods for automated genome-scale metabolic model reconstruction". United States. https://doi.org/10.1042/BST20170246. https://www.osti.gov/servlets/purl/1493924.
@article{osti_1493924,
title = {Methods for automated genome-scale metabolic model reconstruction},
author = {Faria, José P. and Rocha, Miguel and Rocha, Isabel and Henry, Christopher S.},
abstractNote = {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.},
doi = {10.1042/BST20170246},
journal = {Biochemical Society Transactions},
number = 4,
volume = 46,
place = {United States},
year = {2018},
month = {7}
}
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