Table 3 Generally the comparative approaches perform much better than MFE methods at determining S. cerevisiae tRNA-PHE structure. For the consensus predictions of RNAalifold and Carnac we also computed "filled" structures using constrained MFE predictions. This usually improved the sensitivity of the methods. PFold a built-in stem-extension procedure to fill structures. As the tRNA structure contains a multi-loop Foldalign is not expected to perform well here. Dynalign performed well on the most diverse data-set (M) but didn't do well on the high similarity data-set. The structure alignment methods generally did poorly here. Most probably due to the miss-folded MFE structure which were used as input. Trimming high entropy base-pairs from the input structures produced modest improvements.
From: A comprehensive comparison of comparative RNA structure prediction approaches
| Â | S. cerevisiae tRNA-PHE: 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) | 21 | 20 | 19 (90.5) | 0 (100.0) | 0.950 (95.2) |
RNAalifold (H) + RNAfold-C | 21 | 21 | 21 (100.0) | 0 (100.0) | 1.000 (100.0) |
RNAalifold (M) | 18 | 14 | 14 (77.8) | 0 (100.0) | 0.880 (88.9) |
RNAalifold (M) + RNAfold-C | 18 | 21 | 18 (100.0) | 0 (100.0) | 1.000 (100.0) |
ILM (H) | 21 | 24 | 16 (76.2) | 7 (69.6) | 0.722 (72.9) |
ILM (M) | 18 | 30 | 18 (100.0) | 6 (75.0) | 0.863 (87.5) |
Pfold (H) | 21 | 21 | 20 (95.2) | 0 (100.0) | 0.975 (97.6) |
Pfold (M) | 18 | 21 | 18 (100.0) | 0 (100.0) | 1.000 (100.0) |
Plan B: Unaligned sequences | |||||
Carnac (H) | 21 | 17 | 15 (71.4) | 1 (93.8) | 0.815 (82.6) |
Carnac (H) + RNAfold-C | 21 | 21 | 19 (90.5) | 1 (95.0) | 0.925 (92.7) |
Carnac (M) | 21 | 13 | 12 (57.1) | 1 (92.3) | 0.722 (74.7) |
Carnac (M) + RNAfold-C | 21 | 22 | 16 (76.2) | 5 (76.2) | 0.757 (76.2) |
Dynalign (H) | 21 | 22.40 | 11.50 (54.78) | 10.20 (54.45) | 0.5353 (54.59) |
Dynalign (M) | 21 | 21.10 | 19.80 (94.27) | 1.20 (95.00) | 0.9448 (94.64) |
Foldalign (H) | 21 | 16 | 5 (23.8) | 11 (31.2) | 0.259 (27.5) |
Foldalign (M) | 21 | 16 | 5 (23.8) | 10 (33.3) | 0.268 (28.6) |
Plan C: Structure alignment | |||||
MARNA (H) | 21 | 19 | 6 (28.6) | 12 (33.3) | 0.295 (31.0) |
MARNA (M) | 21 | 22 | 7 (33.3) | 15 (31.8) | 0.311 (32.6) |
MARNA-trim (H) | 21 | 6 | 6 (28.6) | 0 (100.0) | 0.530 (64.3) |
MARNA-trim (M) | 21 | 15 | 15 (71.4) | 0 (100.0) | 0.843 (85.7) |
RNAforester (H) | 21 | 23 | 6 (28.6) | 16 (27.3) | 0.263 (27.9) |
RNAforester (M) | 21 | 21 | 14 (66.7) | 7 (66.7) | 0.659 (66.7) |