Locally installed RNAfold does not color the predicted secondary structure

Question

[S]

Hi Everyone,

I downloaded a command line version of the RNAfold package on linux server and I am trying to predict the secondary structure of the RNAs. Everything is working fine except the predicted secondary structure is has no color annotations (it is black and white) unlike the secondary structure predicted using the RNAfold webserver. I read online and checked all the options but I can not find an option to have color included in the structure. Has anyone come across this issue or has a suggestion?

Thank you in advance for your time and suggestions.

Answer 1

[Pierre Lindenbaum]

https://www.tbi.univie.ac.at/RNA/tutorial/

The --pre tag adds PostScript code to color distinct regions of your molecule.

?

[S]

Thanks, Pierre! Do you know of a way to color it using "base-pairing probabilities" just like the structure produced by the RNAfold webserver?