TNA4OptFlux : a software tool for the analysis of strain optimization strategies
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/25072 |
Resumo: | BACKGROUND:Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes' production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved.FINDINGS:We introduce a software tool, the Topological Network Analysis for OptFlux (TNA4OptFlux), a plug-in which adds to the open-source ME platform OptFlux the capability of creating and performing topological analysis over metabolic networks. One of the tool's major advantages is the possibility of using these tools in the analysis and comparison of simulated phenotypes, namely those coming from the results of strain optimization algorithms. We illustrate the capabilities of the tool by using it to aid the interpretation of two E. coli strains designed in OptFlux for the overproduction of succinate and glycine.CONCLUSIONS:Besides adding new functionalities to the OptFlux software tool regarding topological analysis, TNA4OptFlux methods greatly facilitate the interpretation of non-intuitive ME strategies by automating the comparison between perturbed and non-perturbed metabolic networks. The plug-in is available on the web site http://www.optflux.org webcite, together with extensive documentation. |
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TNA4OptFlux : a software tool for the analysis of strain optimization strategiesStrain optimizationMetabolic networksTopological analysisOpen-source softwareOptFluxBACKGROUND:Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes' production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved.FINDINGS:We introduce a software tool, the Topological Network Analysis for OptFlux (TNA4OptFlux), a plug-in which adds to the open-source ME platform OptFlux the capability of creating and performing topological analysis over metabolic networks. One of the tool's major advantages is the possibility of using these tools in the analysis and comparison of simulated phenotypes, namely those coming from the results of strain optimization algorithms. We illustrate the capabilities of the tool by using it to aid the interpretation of two E. coli strains designed in OptFlux for the overproduction of succinate and glycine.CONCLUSIONS:Besides adding new functionalities to the OptFlux software tool regarding topological analysis, TNA4OptFlux methods greatly facilitate the interpretation of non-intuitive ME strategies by automating the comparison between perturbed and non-perturbed metabolic networks. The plug-in is available on the web site http://www.optflux.org webcite, together with extensive documentation.This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within projects ref. COMPETE FCOMP-01-0124-FEDER-015079 and PEst-OE/EEI/UI0752/2011. JPP and RP work is funded by PhD grants from the Portuguese FCT (ref. SFRH/BD/41763/ 2007 and SFRH/BD/51111/2010).BioMed CentralUniversidade do MinhoPinto, José P.Pereira, RuiCardoso, JoãoRocha, I.Rocha, Miguel20132013-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/25072eng1756-050010.1186/1756-0500-6-17523641878info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:09:03Zoai:repositorium.sdum.uminho.pt:1822/25072Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:00:24.674428Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
title |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
spellingShingle |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies Pinto, José P. Strain optimization Metabolic networks Topological analysis Open-source software OptFlux |
title_short |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
title_full |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
title_fullStr |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
title_full_unstemmed |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
title_sort |
TNA4OptFlux : a software tool for the analysis of strain optimization strategies |
author |
Pinto, José P. |
author_facet |
Pinto, José P. Pereira, Rui Cardoso, João Rocha, I. Rocha, Miguel |
author_role |
author |
author2 |
Pereira, Rui Cardoso, João Rocha, I. Rocha, Miguel |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Pinto, José P. Pereira, Rui Cardoso, João Rocha, I. Rocha, Miguel |
dc.subject.por.fl_str_mv |
Strain optimization Metabolic networks Topological analysis Open-source software OptFlux |
topic |
Strain optimization Metabolic networks Topological analysis Open-source software OptFlux |
description |
BACKGROUND:Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes' production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved.FINDINGS:We introduce a software tool, the Topological Network Analysis for OptFlux (TNA4OptFlux), a plug-in which adds to the open-source ME platform OptFlux the capability of creating and performing topological analysis over metabolic networks. One of the tool's major advantages is the possibility of using these tools in the analysis and comparison of simulated phenotypes, namely those coming from the results of strain optimization algorithms. We illustrate the capabilities of the tool by using it to aid the interpretation of two E. coli strains designed in OptFlux for the overproduction of succinate and glycine.CONCLUSIONS:Besides adding new functionalities to the OptFlux software tool regarding topological analysis, TNA4OptFlux methods greatly facilitate the interpretation of non-intuitive ME strategies by automating the comparison between perturbed and non-perturbed metabolic networks. The plug-in is available on the web site http://www.optflux.org webcite, together with extensive documentation. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013 2013-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/25072 |
url |
http://hdl.handle.net/1822/25072 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1756-0500 10.1186/1756-0500-6-175 23641878 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799132399544565760 |