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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

  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)