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Reconstructing High-Quality Large-Scale Metabolic Models with merlin

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Metabolic Network Reconstruction and Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

Abstract

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 a 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) among others.

This tutorial covers each feature of merlin in detail, including the assessment of experimental data for the validation of the model.

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Author information

Authors and Affiliations

  1. Centre of Biological Engineering, University of Minho, Braga, Portugal

    Oscar Dias, Miguel Rocha, Eugénio Campos Ferreira & Isabel Rocha

Authors
  1. Oscar Dias
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  2. Miguel Rocha
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  3. Eugénio Campos Ferreira
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  4. Isabel Rocha
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Corresponding author

Correspondence to Oscar Dias .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

1 Electronic Supplementary Material

Fig. S1

NCBI assembly webpage. The genome can be accessed from the links on the right (GenBank—green arrow; RefSeq—dashed green arrow). Below other relevant links. The link inside the red ellipse allows retrieving the taxonomy identifier (blue circle) from the NCBI taxonomy database (PDF 723 kb)

Fig. S2

InterProScan report. Red circle—submenu for accessing the report. Genes with InterProScan’s reports are noticeable by buttons with purple background (PDF 471 kb)

Fig. S3

Transporters annotation panel. Black circle—information types available in the information window; Red ellipse—integrate similarity information with TRIAGE’s TAD; blue ellipse—create transport reactions; green ellipse—integrate to model or export information to tabular file. The information panel shows several ontology reactions, derived from the primary transporters’ annotations (PDF 418 kb)

Fig. S4

Compartments annotation panel. Secondary compartments may be annotated if the score is close to the one of the main compartments (PDF 367 kb)

Fig. S5

Growth rate versus ATP flux. The slope represents the growth ATP requirements and the y-intercept value indicates the maintenance ATP flux (PDF 28 kb)

Fig. S6

merlin’s main interface. The main interface has three main components, namely the operation bar (blue square), the clipboard (green square), and the data visualizer (red square) (PDF 187 kb)

Fig. S7

RefSeq multispecies annotation (PDF 262 kb)

Fig. S8

Flowchart for the annotation of new transporters from TCDB (PDF 206 kb)

Fig. S9

Example of plots for determining the specific growth rate (a) and specific consumption rate (b). In the former only the first five data points should be selected to perform the linear regression as the other do not belong to the exponential growth phase (PDF 94 kb)

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Dias, O., Rocha, M., Ferreira, E.C., Rocha, I. (2018). Reconstructing High-Quality Large-Scale Metabolic Models with merlin. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_1

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

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