Finding the Length of YOYO-Stained DNA

We frequently need to find the length of a DNA molecule. This is trickier than it sounds because the YOYO-staining produced a non-uniform signal along the length of the DNA molecule.

1. My Approach

The code below takes the following approach to dealing with non-uniform YOYO-signal:

1. The DNA signal is smoothed via a 7-point median filter.

2. The DNA signal is fit to the following sigmoidal (logistic) function with five adjustable parameters:

   y = A · [ 1 / (1 + b·e^−cx) + 1 / (1 + b·e^{c(x − w)}) ] + y₀

   where A is the amplitude; b and c determine the x-offset and curvature; w is related to the width of the DNA; and y₀ is the y-offset.

3. After the best parameters are found, the DNA length is defined as the FWHM of the model data.

2. Code

• dna_lengths.m - Finds DNA lengths by fitting the data to a logistic function
• fwhm.m - Finds FWHM of a signal. Original routine (from Matlab Central File Exchange) was modified by Ilya.