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Table 5 RNase P is a difficult data-set to study. Five sequences in the high similarity data-set are truncated at both the 5 and 3 prime ends (due to the primers used for sequencing these). Sequences in the medium similarity data-set are full-length but do not align well using traditional tools such as ClustalW. Values corresponding to the re-evaluation of ILM with pseudo-knot inclusive reference structures are indicated by "ILM-pknot".

From: A comprehensive comparison of comparative RNA structure prediction approaches

  E. coli RNase P: Comparative Methods
Algorithm number of bps in reference number of bps in prediction True Positives (% sensitivity) False Positives (% selectivity) Correlation (%)
RNAalifold (H) 71 113 56 (78.9) 16 (77.8) 0.782 (78.3)
RNAalifold (H) + RNAfold-C 71 119 55 (77.5) 16 (77.5) 0.773 (77.5)
RNAalifold (M) 54 66 31 (57.4) 23 (57.4) 0.571 (57.4)
RNAalifold (M) + RNAfold-C 54 77 33 (61.1) 16 (67.3) 0.639 (64.2)
Pfold (H) 71 67 47 (66.2) 6 (88.7) 0.765 (77.4)
Pfold (M) 54 87 47 (87.0) 4 (92.2) 0.895 (89.6)
ILM (H) 71 124 31 (43.7) 54 (36.5) 0.395 (40.1)
ILM (M) 54 133 38 (70.4) 31 (55.1) 0.620 (62.7)
ILM-pknot (H) 110 124 53 (48.2) 65 (44.9) 0.463 (46.5)
ILM-pknot (M) 110 133 44 (40.0) 75 (37.0) 0.382 (38.5)
Plan B: Unaligned sequences
Carnac (H) 71 40 36 (50.7) 0 (100.0) 0.712 (75.4)
Carnac (H) + RNAfold-C 71 116 50 (70.4) 25 (66.7) 0.684 (68.5)
Carnac (M) 97 80 63 (64.9) 3 (95.5) 0.787 (80.2)
Carnac (M) + RNAfold-C 97 118 78 (80.4) 25 (75.7) 0.779 (78.1)
Foldalign (H) 71 41 14 (19.7) 25 (35.9) 0.265 (27.8)
Foldalign (M) 97 24 5 (5.2) 17 (22.7) 0.107 (13.9)
Dynalign (H) 71 95.13 28.63 (40.31) 41.50 (39.59) 0.3974 (39.96)
Dynalign (M) 97 103.20 31.00 (31.95) 61.50 (32.80) 0.3208 (32.39)
Plan C: Structure alignment
MARNA (H) 71 89 37 (52.1) 23 (61.7) 0.566 (56.9)
MARNA (M) 97 60 48 (49.5) 9 (84.2) 0.645 (66.8)
MARNA-trim (H) 71 52 37 (52.1) 3 (92.5) 0.694 (72.3)
MARNA-trim (M) 97 43 39 (40.2) 1 (97.5) 0.625 (68.9)
RNAforester (H) 71 114 40 (56.3) 31 (56.3) 0.562 (56.3)
RNAforester (M) 97 117 64 (66.0) 44 (59.3) 0.624 (62.6)