https://github.com/almaaslab/carvefungi

Science Score: 13.0%

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Repository

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Host: GitHub
Owner: AlmaasLab
License: gpl-3.0
Default Branch: main
Size: 2.41 MB

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Fork of SandraCastilloPriego/CarveFungi

Created about 5 years ago · Last pushed over 5 years ago

https://github.com/AlmaasLab/CarveFungi/blob/main/

# 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.

Requirements:
- Tensorflow
- keras
- biopython
- pandas
- numpy
- cobrapy
- Framed (https://github.com/cdanielmachado/framed)
- EggNog annotation software: https://github.com/eggnogdb/eggnog-mapper
- Download the deep learning models from "http://doi.org/10.5281/zenodo.4436488" and copy them into the folder "/bin/compartmentPredictions/deepModels".


 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](/images/CNN.png)

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.

Owner

Name: AlmaasLab
Login: AlmaasLab
Kind: organization
Email: eivind.almaas@ntnu.no
Location: Trondheim, Norway

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