The R Journal: accepted article

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G2F as a Novel Tool to Find and Fill Gaps in Metabolic Networks PDF download
Daniel Osorio, Andrés Pinzón Velasco, Nicolás Mendoza-Mejía, Felipe Rojas-Rodríguez and Janneth González

Abstract During the building of a genome-scale metabolic model, there are several dead-end metabo lites and substrates which cannot be imported, produced nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from dead-end metabolites and fill them from the stoichiometric reactions of a reference, filtering candidate reactions using a weighting function. Additionally, this algorithm allows to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database. Our package is compatible with both 4.0.0 and 3.6.0 R versions.

Received: 2019-10-20; online 2021-07-15


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@article{RJ-2021-064,
  author = {Daniel Osorio and Andrés Pinzón Velasco and Nicolás Mendoza-
          Mejía and Felipe Rojas-Rodríguez and Janneth
          González},
  title = {{G2F as a Novel Tool to Find and Fill Gaps in Metabolic
          Networks}},
  year = {2021},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2021-064},
  url = {https://journal.r-project.org/archive/2021/RJ-2021-064/index.html}
}