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dc.contributor.authorDias, Oscarpor
dc.contributor.authorRocha, Miguelpor
dc.contributor.authorFerreira, E. C.por
dc.contributor.authorRocha, I.por
dc.identifier.citationDias, O.; Rocha, Miguel; Ferreira, E. C.; Rocha, I., Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research, 43(8), 3899-3910, 2015por
dc.description.abstractThe 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.por
dc.description.sponsorshipPhD 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).por
dc.publisherOxford University Presspor
dc.titleReconstructing genome-scale metabolic models with merlinpor
oaire.citationConferencePlaceUnited Kingdom-
oaire.citationTitleNucleic acids researchpor
dc.subject.wosScience & Technologypor
sdum.journalNucleic acids researchpor
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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