I have used PSI-Pred to generate secondary structure predictions of each scanned alanine mutation. How do I compile all this data to look for significant deviations from the wild-type protein?
My approach was to use a sliding window (say 5 amino acids wide) and take a weighted average with respect to the centre amino acid. From this, I wasn't sure how to proceed. Maybe I could take all the averages from matching window positions and use the average to run a t-test against the wild-type.
Can you impart some wisdom?