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RNAfold with batch constraints

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?

rnafold viennarna package
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updated by bounlu bounlu • written by fer.martin.alonso • fer.martin.alonso

1 answer

You can use:

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

as explained here.

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written by bounlu bounlu

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