Table 3.
Grammar performance.
| Sensitivity % (PPV %) | ||||
| Grammar |
Full Benchmarking Set Sensitivity % (PPV %) |
RNase P | SRP | tmRNA |
| G1 | 17 (12) | 14 (11) | 37 (32) | 10(6) |
| G3 | 34 (31) | 37 (35) | 28 (28) | 31 (22) |
| G4 | 10 (8) | 10(8) | 19 (17) | 4(2) |
| G5 | 3(4) | 3(4) | 2(3) | 4(3) |
| G6 | 47 (45) | 49 (49) | 47 (49) | 44 (33) |
| G2 | 36 (25) | 31 (23) | 59 (48) | 33 (17) |
| G7 | 45 (43) | 46 (46) | 50 (52) | 40 (30) |
| G8 | 46 (44) | 46 (46) | 52 (53) | 44 (32) |
| G6S | 49 (45) | 50 (50) | 50 (51) | 44 (32) |
| mfold v3.1.2 | 56 (48) | 56 (51) | 70 (66) | 46 (30) |
| Vienna RNA | 55 (47) | 55 (51) | 67 (64) | 45 (30) |
| PKNOTS | 50 (41) | 53 (46) | 58 (55) | 38 (24) |
| RNAstructure | 56 (47) | 58 (52) | 62 (58) | 46 (30) |
| Pfold | 39 (69) | 42 (76) | 35 (64) | 33 (54) |
The first section contains simple grammars, the second contains stacking grammars, and the last section contains other available software packages that predict secondary structure. The nine grammars were trained on rRNA as described in the text. The second column gives the performance on the full benchmarking dataset, which is subdivided into each family in the subsequent columns. The metrics are calculated over base pairs as described in the text, evaluating the metrics over individual sequences shows similar results (data not shown).