Team:Alberta/Project/Modeling/FindEssentialGenes

%Any single gene knockout resulting in a growth rate less than CutOffCoeff*InitialGrowthRate will be put into a list function [Essentials,grRatio,grRateKO,grRateWT,hasEffect,fluxSolution] = FindEssentialGenes(Model,CutOffCoeff) Essentials=cell(1); b=1; solution1 = optimizeCbModel(Model, 'max', 'false', 'false'); InitialGrowthRate = solution1.f CutOffGrowthRate=CutOffCoeff*InitialGrowthRate; [grRatio,grRateKO,grRateWT,hasEffect,fluxSolution]=singleGeneDeletion(Model); %This part uses the results of singleGeneDeletion to make a list %containing all of the genes whose deletion caused a growth rate less than %CutOffGrowthRate for a=(1:length(grRateKO)) if grRateKO(a)<CutOffGrowthRate Essentials(b) = Model.genes(a); b=b+1; end end NumberOfEssentialGenes = length(Essentials) Essentials = Essentials';