Dwell time analysis of single-molecule force-spectroscopy data.
(c) 2020 Cesar Lopez Pastrana
This software was used in the work "Dynamics of DNA nicking and unwinding by the RepC–PcrA complex" Carolina Carrasco, Cesar L Pastrana, Clara Aicart-Ramos, Sanford H Leuba, Saleem A Khan, Fernando Moreno-Herrero Nucleic Acids Research, 48(4), 2020: 2013–2025.
These codes are Linux-based and are executed at terminal level.
Single-molecule extension traces and codes have to be located on the same path. Traces files can have any name but they must be .txt in extension. Each trace file contains (in columns) time, the extension of a translocation experiment, starting time of translocation (single row) and the time when translocation is finished (single row). In other words, the output of head my_trace_data.txt should be similar to:
Time(s) Extension(um) t0(s) tf(s)
0.017 1.52721 25.0 132.0
0.033 1.55897
0.005 1.60012
0.067 1.59097
where the useful data in terms of dwell time analysis is located between times 25 and 132 seconds. To execute the analysis simply go to the terminal and run the main script
./dt_analysis.sh
This script parses the data to the Octave function dt_analysis.m. The bash script and Octave work synergistically to load, filter and pre-analyze the data. The MATLAB file can be edited to change the the filtering window (points for the moving average or median filter) as well as the extension step for the analysis of dwell times. Finally, the function dwell_time.m executes the dwell time analysis for a given file previoulsy processed by dt_analysis.m. The software produces the file 'dwell_times.dat' which contains a list of all the dwell times. Finally, the main bash script generates dwell times histograms, saved as 'dwell_time_histogram.dat', extract statistics and and calls Gnuplot for data reppresentation and fitting.