Table 3 The accuracy of secondary structure models predicted from the sequence of K-turn–GNRA construct (best values in bold)
From: New in silico approach to assessing RNA secondary structures with non-canonical base pairs
Method | PPV | TPR | MCC |
|---|---|---|---|
Variant I: Canonical and non-canonical base pairs | |||
RNAwolf | 0.67 | 0.44 | 0.54 |
MC-Fold-DP | 0.85 | 0.61 | 0.72 |
MC-Fold | 0.77 | 0.56 | 0.65 |
RC/Rp-1 | 1.00 | 0.67 | 0.82 |
RC/Rp-2 | 1.00 | 0.72 | 0.85 |
RC/Rp-3 | 1.00 | 0.67 | 0.82 |
Variant II: Canonical base pairs only | |||
RNAwolf | 0.70 | 0.78 | 0.74 |
MC-Fold-DP | 0.69 | 1.00 | 0.83 |
MC-Fold | 0.89 | 0.89 | 0.89 |
RC/Rp-1 | 1.00 | 1.00 | 1.00 |
RC/Rp-2 | 1.00 | 1.00 | 1.00 |
RC/Rp-3 | 1.00 | 0.89 | 0.94 |
Variant III: Non-canonical base pairs only, regardless of classification | |||
RNAwolf | 0.50 | 0.11 | 0.24 |
MC-Fold-DP | n/a | 0 | n/a |
MC-Fold | 1.00 | 0.11 | 0.33 |
RC/Rp-1 | 1.00 | 0.33 | 0.58 |
RC/Rp-2 | 1.00 | 0.44 | 0.67 |
RC/Rp-3 | 0.75 | 0.33 | 0.50 |
Variant IV: Non-canonical base pairs only, classification dependent | |||
RNAwolf | 1.00 | 0.11 | 0.33 |
MC-Fold-DP | n/a | n/a | n/a |
MC-Fold | 1.00 | 0.11 | 0.33 |
RC/Rp-1 | 0.67 | 0.25 | 0.41 |
RC/Rp-2 | 0.75 | 0.38 | 0.53 |
RC/Rp-3 | 0.67 | 0.25 | 0.41 |