Reconstructing genome-scale metabolic models with merlin
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/1822/35204 |
Resumo: | The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin. |
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Reconstructing genome-scale metabolic models with merlinScience & TechnologyThe Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.PhD grant to O. D. [SFRH /BD/47307/2008]; ERDF-European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness); National Funds through the FCT within the projects FCOMP-01-0124-FEDER-009707 (HeliSysBio-molecular Systems Biology in Helicobacter pylori) and FCOMP-01-0124-FEDER-015079 (ToMEGIM-Computational Tools for Metabolic Engineering using Genome-scale Integrated Models).Oxford University PressUniversidade do MinhoDias, OscarRocha, MiguelFerreira, Eugénio C.Rocha, I.20152015-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/35204engDias, O.; Rocha, Miguel; Ferreira, E. C.; Rocha, I., Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research, 43(8), 3899-3910, 20150305-10481362-496210.1093/nar/gkv29425845595http://nar.oxfordjournals.org/info: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:RCAAP2023-07-21T12:10:58Zoai:repositorium.sdum.uminho.pt:1822/35204Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:02:39.825958Repositório 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 |
Reconstructing genome-scale metabolic models with merlin |
title |
Reconstructing genome-scale metabolic models with merlin |
spellingShingle |
Reconstructing genome-scale metabolic models with merlin Dias, Oscar Science & Technology |
title_short |
Reconstructing genome-scale metabolic models with merlin |
title_full |
Reconstructing genome-scale metabolic models with merlin |
title_fullStr |
Reconstructing genome-scale metabolic models with merlin |
title_full_unstemmed |
Reconstructing genome-scale metabolic models with merlin |
title_sort |
Reconstructing genome-scale metabolic models with merlin |
author |
Dias, Oscar |
author_facet |
Dias, Oscar Rocha, Miguel Ferreira, Eugénio C. Rocha, I. |
author_role |
author |
author2 |
Rocha, Miguel Ferreira, Eugénio C. Rocha, I. |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Dias, Oscar Rocha, Miguel Ferreira, Eugénio C. Rocha, I. |
dc.subject.por.fl_str_mv |
Science & Technology |
topic |
Science & Technology |
description |
The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015 2015-01-01T00:00:00Z |
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 |
https://hdl.handle.net/1822/35204 |
url |
https://hdl.handle.net/1822/35204 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Dias, O.; Rocha, Miguel; Ferreira, E. C.; Rocha, I., Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research, 43(8), 3899-3910, 2015 0305-1048 1362-4962 10.1093/nar/gkv294 25845595 http://nar.oxfordjournals.org/ |
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 |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
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 |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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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 |
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1799132429445758976 |