Skip to main content

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

  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)