Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks



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Supporting Information


S1 Table. Main characteristics of a panel of gap-filling methods.

(PDF)


S1 Appendix. Description of the different methods used in the benchmark and a more precised description of the obtained results.

(PDF)


S1 Files. E. coli benchmark of 10,800 non-functional degraded networks and FVA results. All files needed to run gap-filling experiments on the benchmark are provided in an archive as well as a Readme.txt file detailing the commands used to produce the results shown in this study. This archive also contains the global results for FVA and a detailed analysis of the network 256 and the biomass 89 as an example. (ZIP)

S2 Files. E. siliculosusnetworks and essential reactions. The two draft networks used to study potential cross-feeding relations between E. siliculosus and Ca. P. ectocarpi are provided together with the list of seeds and targets used to run the Meneco tool. The exhaustive analysis of essential reactions which allow the production of 83 target metabolites thanks to the combination of E. siliculosus and Ca. P. ectocarpi networks is provided in a separate file. Finally, detailled examples of false positive predicted interactions and their explanation are provided in a separate pdf file. (ZIP)

S3 Files. E. mutabilis networks. Both draft and functional reconstructed metabolic networks for E. mutabilis are provided here. The folder also provides the SBML file describing the repair database (MetaCyc 17.5 modified as described in the Material and Methods) required to run the Meneco tool. Files corresponding to targets and seeds are also provided. The file seed_minimum_medium_Emutabilis.sbml describes light and the 8 mineral nutrients of the minimal growth medium for E. mutabilis. As described in the main text, the network is not functional with only these seeds as reactions in cycles are blocked. The file “seeds_min_Emutabilis_final. sbml” provides the minimal set of seeds necessary to unblock the cycles and produce all the targets in “targets_Emutabilis_72.sbml” while the list of seeds and targets is also provided as tables in the file “seedsAndTargets_euglena.pdf”. (ZIP)

Author Contributions


Conceptualization: SP SMD ST AL GC DE JB FP TT AS.

Data curation: SP CF SMD AL GC FP.

Funding acquisition: AS TT.

Investigation: SP CF SMD AL GC FG JB FP TT AS.

Methodology: SP SMD ST AL GC FG DE JB FP TT AS.

Project administration: SP AS.

Software: SP ST GC AS.

Supervision: SMD DE FP TT AS.

Validation: SP CF SMD ST FG FP TT AS.

Visualization: SP CF SMD GC FG FP TT AS.

Writing – original draft: SP CF SMD ST AL GC FP TT AS.

Writing – review & editing: SP CF SMD ST AL GC FG JG DE JB FP TT AS.

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