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A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, Sebastián N. ; Olivier, Brett G. ; Molenaar, Douwe ; Teusink, Bas

In: Genome Biology, 20 (2019), Nr. 158. pp. 1-20. ISSN 1474-760X

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Abstract

Background: Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research.

Results: In this work, we perform a systematic assessment of current genome-scale reconstruction software platforms. To meet our goal, we first define a list of features for assessing software quality related to genome-scale reconstruction. Subsequently, we use the feature list to evaluate the performance of each tool. To assess the similarity of the draft reconstructions to high-quality models, we compare each tool’s output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We additionally compare draft reconstructions with a model of Pseudomonas putida to further confirm our findings. We show that none of the tools outperforms the others in all the defined features.

Conclusions: Model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model. They can use this benchmark study as a guide to select the best tool for their research. Finally, developers can also benefit from this evaluation by getting feedback to improve their software.

Item Type: Article
Journal or Publication Title: Genome Biology
Volume: 20
Number: 158
Publisher: BioMed Central
Place of Publication: London
Date Deposited: 21 Aug 2019 10:48
Date: 2019
ISSN: 1474-760X
Page Range: pp. 1-20
Faculties / Institutes: Service facilities > Bioquant
Service facilities > Centre for Organismal Studies Heidelberg (COS)
Subjects: 610 Medical sciences Medicine
Uncontrolled Keywords: Genome-scale metabolic reconstruction, Systematic evaluation, Genome-scale metabolic models, Bordetella pertussis, Lactobacillus plantarum, Pseudomonas putida
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