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TitleReconstructing high-quality large-scale metabolic models with merlin
Author(s)Dias, Oscar
Rocha, Miguel
Ferreira, Eugénio C.
Rocha, Isabel
KeywordsGenome functional annotation
Genome-scale metabolic models
Transport proteins annotation
Issue date7-Jan-2018
JournalMethods in Molecular Biology
CitationDias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel, Reconstructing high-quality large-scale metabolic models with merlin. In Marco Fondi, Metabolic Network Reconstruction and Modeling: Methods and Protocols, Vol. Methods in Molecular Biology 1716, Springer, 2018. ISBN: 978-1-4939-7528-0, 1-36
Abstract(s)Here the basic principles of reconstructing genome-scale metabolic models with merlin are described. This tool covers the basic stages of this process, providing several tools that allow assembling models, using the sequenced genome as starting point. merlin has two main modules, separating the process of annotating (enzymes, transporters and compartments) on the genome from the process of model assembly, though information from the former is integrated in the latter after curation. Moreover, merlin provides several tools to curate the model, including tools for generating reactions gene rules and placeholder entities for biomass precursors, such as proteins (e-protein) or nucleotides (e-DNA and e-RNA) amongst others. This tutorial covers each feature of merlin in detail, including the assessment of experimental data for validation of the model.
TypeBook part
Publisher version
AccessRestricted access (UMinho)
Appears in Collections:CEB - Livros e Capítulos de Livros / Books and Book Chapters

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Table S.1447,49 kBAdobe PDFView/Open
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Chapter1,36 MBAdobe PDFView/Open

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