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TitleReconstructing genome-scale metabolic models with merlin
Author(s)Dias, Oscar
Rocha, Miguel
Ferreira, E. C.
Rocha, I.
Issue date2015
PublisherOxford University Press
JournalNucleic acids research
CitationDias, O.; Rocha, Miguel; Ferreira, E. C.; Rocha, I., Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Research, 43(8), 3899-3910, 2015
Abstract(s)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.
Publisher version
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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