MATLAB scripts

All scripts can be downloaded from the following .zip file: Federica_Computation_Folder.zip.

uniform_inters.m

Inputs	seq: sequence
	lambda: lambda values
	M: desired number of links
Parameters	model for DNA: `models = "cgDNA+min"`
	closure assumption: `boundaries = "PC"`
	sequence: `seq`: the sequence `seq_name`: the name of the sequence
Outputs	the configuration with the desired number of links M
Outputs	2D plots of lambda values versus the number of links m

The function computes the gradient of the Lagrangian function depending on a variable z for each lambda received as imput. Then it finds its singular value with the mldivide method and compute the number of links corresponding with the obtained configuration. The cycle stops when it finds the configuration with the requested number of links M.

test_script.m

In this script you can decide the sequence, the lambda values and the number of links M and it runs the runs the function uniform_inters.m. It has just the aim of test and try the function uniform_inters.m.

The bBDNA software can be found on the LVCMM software page: link.