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
| Â | 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) |