About TrimGdel
TrimGdel aims to find the smallest gene deletion strategy for growth coupled production by removing unnecessary gene deletions from a large gene deletion strategy obtained by gDel_minRN for a given target metabolite and constraint-based model.
Necessary environments
An environment where MATLAB, CPLEX, COBRA Toolbox can run is required.
Run the test code for TrimGdel
The test code is run by the following command:
test()
“test()” loads a MATLAB matfile “e_coli_core.mat” containing a core metabolic model of E.coli, and employs “TrimGdel” to obtain the small gene deletion strategy for growth coupling of succinate.
Example code “example1” employs TrimGdel to calculate a gene deletion strategy for biotin (btn_c) in iML1515.
load(‘iML1515.mat’)
[success, gvalue3, finalGRPR, size1, size2, size3]=TrimGdel(iML1515, ’btn_c’)
In the output, “gvalue3” includes the 0/1 vector indicating which genes should be deleted.
0: genes to be deleted. 1: genes to remain.
Details are described in the comments in the source codes.
T. Tamura, "Trimming gene deletion strategies for growth-coupled production in constraint-based metabolic networks: TrimGdel," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022, doi: 10.1109/TCBB.2022.3185221.