Figure 3

Scoring pipeline. The pipeline illustrates the flow of base pair probabilities during the structure scoring. The PETcofold pipeline consists of two steps: (a) intra-molecular folding by PETfold of both alignments and selection of a set of highly reliable base pairs that form the partial structures σ^p; (b) inter-molecular folding by an adaptation of PETfold of the concatenated alignments using the constraints from Step 1. In the end, (c) the partial structures and constrained inter-molecular structures are combined to generate the joint secondary structure including pseudoknots.