RNAfold with batch constraints

Question

[fer.martin.alonso]

Hi,

I'm new using RNAfold and I am trying to fold sequences of variable length (between 50 and 150bp) and I want to fold them in batch with certain constraints. All sequences share the same restrictions for folding but are of different lengths, therefore the dot-bracket notation would not apply. Any suggestions?

Answer 1

[Ömer An]

You can use:

$ RNAfold --constraint=constraints.txt --batch < sequences.fa

as explained here.