Code to predict first label positions in DNA constructs obtained by "mega primer" PCR assembly, convert the label positions to step size distributions, and to fit experimental step size data using simulated step size distributions.
The code is first described by
Yi-Yun Lin, Tine Brouns, Pauline J. Kolbeck, Willem Vanderlinden, and Jan Lipfert
"High-yield, ligation-free assembly of DNA constructs with nucleosome
positioning sequence repeats for single molecule manipulation assays"
Submitted
Preprint available at
https://www.biorxiv.org/content/10.1101/2023.01.05.522917v1
There are two Matlab scripts:
- Lin_etal_predict_steps.m is used to generate the step size distribution. It can be run stand alone. Simulation parameters are specified in the script.
It outputs a plot of the simulated step size distribution and also writes the simulated steps to a text file.
- Lin_etal_fit_step_distribution.m reads in simulated steps for different values of the label probability from files in the sub-directory "simulated_distributions".
An example set of simulated step sizes is included in the package. More steps (e.g. for different label probabilities, different sequences, etc.) can readily be computed using the first script Lin_etal_predict_steps.m.
The script Lin_etal_fit_step_distribution.m then reads in experimental data, an example of which is provided as Experimental_Steps_45pN.txt.
The script then compared the simulated distributions to the experimental data using both a chi-squared criterion and the mean step size.
The output are plots that are also exported to png and eps files. Example outputs are included in the package.
