Table 9 Pfold predictions on both the high and medium similarity data-sets underflow on E. coli LSU rRNA. RNAalifold and Carnac, however, produce reasonable results.
From: A comprehensive comparison of comparative RNA structure prediction approaches
| Â | E. coli LSU 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) | 794 | 879 | 627 (79.0) | 195 (76.3) | 0.776 (77.6) |
RNAalifold (H) + RNAfold-C | 794 | 871 | 629 (79.2) | 185 (77.3) | 0.782 (78.2) |
RNAalifold (M) | 819 | 721 | 614 (75.0) | 53 (92.1) | 0.831 (83.5) |
RNAalifold (M) + RNAfold-C | 819 | 790 | 691 (84.4) | 78 (89.9) | 0.871 (87.1) |
Pfold (H) | 794 | 0 | 0 (0.0) | 0 (0.0) | 0.000 (0.0) |
Pfold (M) | 819 | 0 | 0 (0.0) | 0 (0.0) | 0.000 (0.0) |
ILM (H) | 794 | 1048 | 389 (49.0) | 602 (39.3) | 0.438 (44.1) |
ILM (M) | 819 | 1161 | 560 (68.4) | 405 (58.0) | 0.630 (63.2) |
ILM-pknot (H) | 869 | 1048 | 272 (31.3) | 759 (26.4) | 0.287 (28.8) |
ILM-pknot (M) | 869 | 1161 | 377 (43.4) | 629 (37.5) | 0.403 (40.4) |
Plan B: Unaligned sequences | |||||
Carnac (H) | 816 | 422 | 390 (47.8) | 7 (98.2) | 0.685 (73.0) |
Carnac (H) + RNAfold-C | 816 | 873 | 674 (82.6) | 156 (81.2) | 0.819 (81.9) |
Carnac (M) | 821 | 508 | 463 (56.4) | 14 (97.1) | 0.740 (76.7) |
Carnac (M) + RNAfold-C | 821 | 865 | 682 (83.1) | 147 (82.3) | 0.827 (82.7) |