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Team:Alberta/Project/Modeling/FindEssentials
From 2009.igem.org
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | %Any single gene knockout resulting in less than CutOffCoeff*InitialGrowthRate | + | %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] = FindEssentials(Model,CutOffCoeff) | function [Essentials,grRatio,grRateKO,grRateWT,hasEffect,fluxSolution] = FindEssentials(Model,CutOffCoeff) | ||
| + | |||
Essentials=cell(1); | Essentials=cell(1); | ||
b=1; | b=1; | ||
solution1 = optimizeCbModel(Model, 'max', 'false', 'false'); | solution1 = optimizeCbModel(Model, 'max', 'false', 'false'); | ||
| - | InitialGrowthRate = solution1.f | + | InitialGrowthRate = solution1.f |
| - | + | CutOffGrowthRate=CutOffCoeff*InitialGrowthRate; | |
[grRatio,grRateKO,grRateWT,hasEffect,fluxSolution]=singleGeneDeletion(Model); | [grRatio,grRateKO,grRateWT,hasEffect,fluxSolution]=singleGeneDeletion(Model); | ||
%This part uses the results of singleGeneDeletion to make a list | %This part uses the results of singleGeneDeletion to make a list | ||
%containing all of the genes whose deletion caused a growth rate less than | %containing all of the genes whose deletion caused a growth rate less than | ||
| - | % | + | %CutOffGrowthRate |
for a=(1:length(grRateKO)) | for a=(1:length(grRateKO)) | ||
| - | if grRateKO(a)< | + | if grRateKO(a)<CutOffGrowthRate |
Essentials(b) = Model.genes(a); | Essentials(b) = Model.genes(a); | ||
b=b+1; | b=b+1; | ||
Latest revision as of 00:45, 18 October 2009
%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] = FindEssentials(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';
