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Title: 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:
 [1];  [2];  [2];  [1]
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
  2. 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) (SC-23)
OSTI Identifier:
1493924
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: 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. doi: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. doi:10.1042/BST20170246.
@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 = {Tue Jul 31 00:00:00 EDT 2018},
month = {Tue Jul 31 00:00:00 EDT 2018}
}

Journal Article:
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Works referenced in this record:

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journal, November 2005

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