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CarveFungi

CarveFungi is a genome-scale metabolic model reconstruction pipeline able to create a compartmentalized metabolic model of any fungal specie from its protein sequences. It is implemented using python.

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CarveFungi uses a deep learning model to predict the cellular localization of the proteins and this information is used to score the reactions. Deep neural network

CarveMe (https://doi.org/10.1093/nar/gky537,https://github.com/cdanielmachado/carveme) uses the scoring of the reactions to obtain a functional metabolic model that is able to produce biomass.

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  • Python 50.3%
  • Jupyter Notebook 49.7%