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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.