Team:WashU StLouis/Software

Washington University - Penn State iGEM

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WashU and Penn State   iGEM 2015
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Singe Gene Knockout Softwares

The Penn State team created a python script to perform single gene knockouts, and determin which genes gave greater metabolic values.


  1. Create a list of all genes, constructed from the provided GPRs in the genome scale model.

  2. Create lists of reactions that will be deleted for each gene knockout. This is done by evaluating each reaction GPR for each gene. If a gene is essential to a given GPR, the reaction is added to the list of reactions which will be deleted for that knockout.

  3. Given a list of deleted reactions for each gene, FBA is run iteratively for each gene knockout. Running FBA will determine maximum biomass, max and min ATP values, and max and min flavodoxin values.

  4. The FBA results are collected and outputted for further analysis.

The code can be found here