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The PETcofold pipeline consists of two steps: (1) intra-molecular folding by PETfold and selection of a set of highly reliable base pairs that only decreases the probability of the ensemble in some pre-defined range; (2) inter-molecular folding by adapted PETfold using constraints from step 1. In the end, partial structures and constrained inter-molecular structures are combined to form the joint RNA secondary structure including pseudoknots.
