Extracting features corresponding to low entropy regions from RNAfold output

Question

[kousi31]

Hi all, I used RNAfold to extract MFE of few long non-codings RNAs and used relplot.pl to visualize the secondary structure. However, I am interested in knowing the regions/locations in base pairs corresponding to the low entropy regions. Is there a way to extract it?

From another biostar post I found a script to extract the features of RNA secondary structure from dotplot, but I don't know how to extract the stable regions corresponding to "low entropy".
Kindly help! Thank you.

[user_without_id]

Do you mean the entropy that relplot apparently shows as hue? Could you pls provide a minimal example?

Answer 1

[khorms]

From RNAfold documentation:

"It also produces PostScript files with plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix. The dot plot shows a matrix of squares with area proportional to the pairing probability in the upper right half, and one square for each pair in the minimum free energy structure in the lower left half. For each pair i−j with probability p>10E−6 there is a line of the form i j sqrt(p) ubox in the PostScript file, so that the pair probabilities can be easily extracted."

So you could write a script that parses the dot.ps probability matrix and then calculate entropy yourself. An example script for parsing dot.ps file can be found here. Otherwise, I don't think there exists a ready-made solution for your problem