Finding hairpin structure

Question

[margo]

Hi, I have a set of sequences (40 nucleotides long). All of the sequences are rho-independent terminators. However, I am interested in finding what structures these sequences form. Is there any software I can use/or parameters I can use to differentiate my findings into hairpin and those that do not form a hairpin?

Answer 1

[JC]

Maybe you can use the ViennaRNA package to fold sequences, write down the structures in text format, and use RegEx scripts to detect hairpin structures.