Fig. 8.

The result on the dataset2 (see Section 3.1.2). ‘Proposed’ means the appro3-1 with the CONTRAfold model and the ProbCons model o α = 1/(1 + |D|) and δ = 0.01. ‘X-Y (M2)’ means the method that predicts a common secondary structure by X after aligning {x}∪D by Y, and then maps the common secondary structure to the target sequence x. ‘raf (M3)’ means the method that simultaneously aligns and folds {x}∪D by using RAF (Do et al., 2008), and then maps the common secondary structure to the target sequence x. ‘centroid’ indicates the γ-centroid estimators (Hamada et al., 2008) for the method (M1) and the averaged γ-centroid estimators (Hamada et al., 2008) for the method (M2), respectively. ‘alifold’ means RNAalifold (Bernhart et al., 2008).