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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

  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)