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SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks

BACKGROUND: High-throughput omics technologies have enabled the comprehensive reconstructions of genome-scale metabolic networks for many organisms. However, only a subset of reactions is active in each cell which differs from tissue to tissue or from patient to patient. Reconstructing a subnetwork...

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Detalles Bibliográficos
Autores principales: Tefagh, Mojtaba, Boyd, Stephen P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158141/
https://www.ncbi.nlm.nih.gov/pubmed/32293238
http://dx.doi.org/10.1186/s12859-020-3440-y
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author Tefagh, Mojtaba
Boyd, Stephen P.
author_facet Tefagh, Mojtaba
Boyd, Stephen P.
author_sort Tefagh, Mojtaba
collection PubMed
description BACKGROUND: High-throughput omics technologies have enabled the comprehensive reconstructions of genome-scale metabolic networks for many organisms. However, only a subset of reactions is active in each cell which differs from tissue to tissue or from patient to patient. Reconstructing a subnetwork of the generic metabolic network from a provided set of context-specific active reactions is a demanding computational task. RESULTS: We propose swiftcc and swiftcore as effective methods for flux consistency checking and the context-specific reconstruction of genome-scale metabolic networks which consistently outperform the previous approaches. CONCLUSIONS: We have derived an approximate greedy algorithm which efficiently scales to increasingly large metabolic networks. swiftcore is freely available for non-commercial use in the GitHub repository at https://mtefagh.github.io/swiftcore/.
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spelling pubmed-71581412020-04-21 SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks Tefagh, Mojtaba Boyd, Stephen P. BMC Bioinformatics Software BACKGROUND: High-throughput omics technologies have enabled the comprehensive reconstructions of genome-scale metabolic networks for many organisms. However, only a subset of reactions is active in each cell which differs from tissue to tissue or from patient to patient. Reconstructing a subnetwork of the generic metabolic network from a provided set of context-specific active reactions is a demanding computational task. RESULTS: We propose swiftcc and swiftcore as effective methods for flux consistency checking and the context-specific reconstruction of genome-scale metabolic networks which consistently outperform the previous approaches. CONCLUSIONS: We have derived an approximate greedy algorithm which efficiently scales to increasingly large metabolic networks. swiftcore is freely available for non-commercial use in the GitHub repository at https://mtefagh.github.io/swiftcore/. BioMed Central 2020-04-15 /pmc/articles/PMC7158141/ /pubmed/32293238 http://dx.doi.org/10.1186/s12859-020-3440-y Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Tefagh, Mojtaba
Boyd, Stephen P.
SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title_full SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title_fullStr SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title_full_unstemmed SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title_short SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks
title_sort swiftcore: a tool for the context-specific reconstruction of genome-scale metabolic networks
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158141/
https://www.ncbi.nlm.nih.gov/pubmed/32293238
http://dx.doi.org/10.1186/s12859-020-3440-y
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