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Table 3 Effects of two different parts that incorporate the structural information

From: Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

    Accuracy of predicted structure (MCC)
Structural pairwise alignment Four-way consistency SPS Pfold McCaskill-MEA RNAalifold
Disabled (globalpair) Disabled 0.768 0.622 0.646 0.622
Disabled (globalpair) Enabled (McCaskill) 0.782 0.674 0.680 0.670
Disabled (globalpair) Enabled (CONTRAfold) 0.781 0.665 0.675 0.668
Enabled (larapair) Disabled 0.758 0.646 0.661 0.630
Enabled (larapair) Enabled (McCaskill) 0.758 0.665 0.692 0.672
Enabled (larapair) Enabled (CONTRAfold) 0.761 0.661 0.689 0.677
Enabled (scarnapair) Disabled 0.787 0.699 0.687 0.693
Enabled (scarnapair) Enabled (McCaskill) 0.789 0.724 0.712 0.726
Enabled (scarnapair) Enabled (CONTRAfold) 0.794 0.711 0.705 0.704
  1. The KKA dataset was used as the benchmark. The accuracies of alignments measured by the SPS criterion are listed in the SPS column. The accuracies of predicted common secondary structures are shown in the three columns on the right. The alignment by each method was subjected to three external prediction programs, Pfold, McCaskill-MEA and RNAalifold, and then the differences from the Rfam curated structure were calculated with the MCC criterion.