Table 5 The 5S rRNA dataset. Base pairs from the top-ranked (NTFirst) motif were used as structural constraints for MFOLD. The table presents the PPV and sensitivity for the application of MFOLD alone as well as the combined approach onto the 5S rRNA dataset. Two setups were used for the combined approach. First, the top-ranked motif, according to NTFirst, was used. Second, a high PPV motif was selected to illustrate the expected benefit for the combined approach. Numbers in between parentheses indicate the number of sub-optimal structures reported with similar performance measures.
From: Identification of consensus RNA secondary structures using suffix arrays
Id | Method | % PPV | % Sensitivity |
|---|---|---|---|
V00336 | MFOLD (2) | 25.0 | 25.6–26.3 |
| Â | Seed NTFirst + MFOLD | 81.1 | 75.0 |
| Â | Seed Best PPV + MFOLD | 62.5 | 67.6 |
| Â | Seed Best PPV + MFOLD | 92.5 | 100.0 |
X02627 | MFOLD (1) | 30.8 | 32.4 |
| Â | MFOLD (1) | 84.6 | 89.2 |
| Â | Seed NTFirst + MFOLD | 75.7 | 71.8 |
| Â | Seed Best PPV + MFOLD | 89.7 | 89.7 |
X04585 | MFOLD (1) | 23.7 | 25.0 |
|  | MFOLD (11) | 18.4 | 20.0–23.3 |
| Â | Seed NTFirst + MFOLD | 60.0 | 55.3 |
| Â | Seed Best PPV + MFOLD | 73.7 | 77.8 |
AJ251080 | MFOLD (1) | 65.8 | 73.5 |
| Â | MFOLD (1) | 60.5 | 65.7 |
|  | MFOLD (2) | 42.1 | 42.1–43.2 |
| Â | MFOLD (1) | 55.3 | 67.7 |
| Â | Seed NTFirst + MFOLD | 66.7 | 63.2 |
| Â | Seed Best PPV+ MFOLD | 71.1 | 75.0 |
| Â | Seed Best PPV + MFOLD | 65.8 | 67.6 |
M25591 | MFOLD (1) | 71.1 | 77.1 |
|  | MFOLD (2) | 42.1 | 43.2–44.4 |
| Â | MFOLD (1) | 60.5 | 71.9 |
| Â | Seed NTFirst + MFOLD | 70.6 | 63.2 |
| Â | Seed Best PPV + MFOLD | 76.3 | 78.4 |