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MP-Align: alignment of metabolic pathways

BACKGROUND: Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction....

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Autores principales: Alberich, Ricardo, Llabrés, Mercè, Sánchez, David, Simeoni, Marta, Tuduri, Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045882/
https://www.ncbi.nlm.nih.gov/pubmed/24886436
http://dx.doi.org/10.1186/1752-0509-8-58
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author Alberich, Ricardo
Llabrés, Mercè
Sánchez, David
Simeoni, Marta
Tuduri, Marc
author_facet Alberich, Ricardo
Llabrés, Mercè
Sánchez, David
Simeoni, Marta
Tuduri, Marc
author_sort Alberich, Ricardo
collection PubMed
description BACKGROUND: Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. RESULTS: We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. CONCLUSION: The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination.
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spelling pubmed-40458822014-06-20 MP-Align: alignment of metabolic pathways Alberich, Ricardo Llabrés, Mercè Sánchez, David Simeoni, Marta Tuduri, Marc BMC Syst Biol Research Article BACKGROUND: Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. RESULTS: We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. CONCLUSION: The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. BioMed Central 2014-05-20 /pmc/articles/PMC4045882/ /pubmed/24886436 http://dx.doi.org/10.1186/1752-0509-8-58 Text en Copyright © 2014 Alberich et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Article
Alberich, Ricardo
Llabrés, Mercè
Sánchez, David
Simeoni, Marta
Tuduri, Marc
MP-Align: alignment of metabolic pathways
title MP-Align: alignment of metabolic pathways
title_full MP-Align: alignment of metabolic pathways
title_fullStr MP-Align: alignment of metabolic pathways
title_full_unstemmed MP-Align: alignment of metabolic pathways
title_short MP-Align: alignment of metabolic pathways
title_sort mp-align: alignment of metabolic pathways
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045882/
https://www.ncbi.nlm.nih.gov/pubmed/24886436
http://dx.doi.org/10.1186/1752-0509-8-58
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