Table 7 The probabilistic approach of PFold can, on occasion, suffer from "under-flow" errors caused by multiplying many probabilities together producing numbers too low to be dealt with on modern computers. This is what has happened on the medium similarity data-set.
From: A comprehensive comparison of comparative RNA structure prediction approaches
| Â | E. coli SSU rRNA: Comparative Methods | ||||
|---|---|---|---|---|---|
Algorithm | number of bps in reference | number of bps in prediction | True Positives (% sensitivity) | False Positives (% selectivity) | Correlation (%) |
Plan A: ClustalW Alignment | |||||
RNAalifold (H) | 460 | 472 | 275 (59.8) | 179 (60.6) | 0.601 (60.2) |
RNAalifold (H) + RNAfold-C | 460 | 483 | 273 (59.3) | 195 (58.3) | 0.588 (58.8) |
RNAalifold (M) | 441 | 433 | 372 (84.4) | 32 (92.1) | 0.881 (88.2) |
RNAalifold (M) + RNAfold-C | 441 | 469 | 388 (88.0) | 44 (89.8) | 0.889 (88.9) |
Pfold (H) | 460 | 377 | 326 (70.9) | 26 (92.6) | 0.810 (81.7) |
Pfold (M) | 441 | 0 | 0 (0.0) | 0 (0.0) | 0.000 (0.0) |
ILM (H) | 460 | 565 | 236 (51.3) | 313 (43.0) | 0.469 (47.1) |
ILM (M) | 441 | 564 | 264 (59.9) | 249 (51.5) | 0.554 (55.7) |
ILM-pknot (H) | 468 | 565 | 236 (50.4) | 311 (43.1) | 0.466 (46.8) |
ILM-pknot (M) | 468 | 564 | 266 (56.8) | 258 (50.8) | 0.537 (53.8) |
Plan B: Unaligned sequences | |||||
Carnac (H) | 460 | 233 | 206 (44.8) | 12 (94.5) | 0.650 (69.6) |
Carnac (H) + RNAfold-C | 460 | 470 | 332 (72.2) | 112 (74.8) | 0.734 (73.5) |
Carnac (M) | 448 | 294 | 259 (57.8) | 18 (93.5) | 0.735 (75.7) |
Carnac (M) + RNAfold-C | 448 | 471 | 337 (75.2) | 110 (75.4) | 0.753 (75.3) |