Table 4.
The MCC, SN and SL values for each method tested in the experiment with sequence alignments of low and medium similarity, as well as the mean and standard deviation of the MCC, SN and SL values for each tool under analysis.
|
KNetFold
|
Pfold
|
RNAalifold
|
RSpredict
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Accession | MCC | SN | SL | MCC | SN | SL | MCC | SN | SL | MCC | SN | SL |
| RF00230 | 0.76 | 0.71 | 0.82 | N/A | N/A | N/A | 0.69 | 0.60 | 0.79 | 0.83 | 0.83 | 0.83 |
| RF00080 | 0.87 | 0.91 | 0.83 | N/A | N/A | N/A | 0.90 | 0.81 | 1.00 | 0.97 | 0.94 | 1.00 |
| RF00515 | 0.84 | 0.71 | 1.00 | N/A | N/A | N/A | 0.81 | 0.66 | 1.00 | 0.96 | 0.93 | 1.00 |
| RF00557 | 1.00 | 1.00 | 1.00 | N/A | N/A | N/A | 0.97 | 0.94 | 1.00 | 0.97 | 0.94 | 1.00 |
| RF00504 | 0.93 | 0.91 | 0.95 | N/A | N/A | N/A | 0.93 | 0.91 | 0.95 | 0.93 | 0.91 | 0.95 |
| RF00029 | 1.00 | 1.00 | 1.00 | N/A | N/A | N/A | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00458 | 0.51 | 0.34 | 0.75 | 0.94 | 0.91 | 0.98 | 0.97 | 0.95 | 0.98 | 0.76 | 0.77 | 0.74 |
| RF00559 | 0.71 | 0.67 | 0.75 | 0.94 | 0.89 | 1.00 | 0.78 | 0.61 | 1.00 | 0.91 | 0.83 | 1.00 |
| RF00234 | 0.92 | 0.84 | 1.00 | 0.94 | 0.89 | 1.00 | 0.97 | 0.97 | 0.97 | 1.00 | 1.00 | 1.00 |
| RF00556 | 0.89 | 0.80 | 1.00 | 0.89 | 0.80 | 1.00 | 0.89 | 0.80 | 1.00 | 0.89 | 0.80 | 1.00 |
| RF00519 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00379 | 0.98 | 0.96 | 1.00 | 0.96 | 0.92 | 1.00 | 0.98 | 0.96 | 1.00 | 0.94 | 0.92 | 0.96 |
| RF00380 | 0.83 | 0.81 | 0.85 | 0.86 | 0.79 | 0.93 | 0.84 | 0.81 | 0.87 | 0.82 | 0.79 | 0.84 |
| RF00445 | 1.00 | 1.00 | 1.00 | 0.94 | 0.89 | 1.00 | 0.96 | 0.93 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00522 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00095 | 0.82 | 0.67 | 1.00 | 0.82 | 0.67 | 1.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
| RF00442 | 1.00 | 1.00 | 1.00 | 0.97 | 0.95 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00430 | 0.97 | 0.93 | 1.00 | 1.00 | 1.00 | 1.00 | 0.98 | 0.97 | 1.00 | 0.93 | 0.93 | 0.93 |
| RF00521 | 1.00 | 1.00 | 1.00 | 0.83 | 0.83 | 0.83 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00049 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00513 | 0.83 | 0.83 | 0.83 | 0.63 | 0.54 | 0.72 | 0.91 | 0.83 | 1.00 | 0.84 | 0.75 | 0.95 |
| RF00309 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00451 | 0.97 | 0.97 | 0.97 | 0.62 | 0.53 | 0.73 | 0.86 | 0.80 | 0.92 | 1.00 | 1.00 | 1.00 |
| RF00464 | 0.94 | 0.88 | 1.00 | 0.53 | 0.35 | 0.82 | 0.94 | 0.88 | 1.00 | 0.92 | 0.85 | 1.00 |
| RF00507 | 1.00 | 1.00 | 1.00 | 0.90 | 0.82 | 1.00 | 0.95 | 0.91 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00388 | 1.00 | 1.00 | 1.00 | 0.91 | 0.82 | 1.00 | 1.00 | 1.00 | 1.00 | 0.99 | 0.97 | 1.00 |
| RF00357 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00434 | 0.70 | 0.62 | 0.78 | 0.50 | 0.45 | 0.57 | 0.82 | 0.76 | 0.88 | 0.85 | 0.79 | 0.92 |
| RF00525 | 0.94 | 0.89 | 1.00 | N/A | N/A | N/A | 0.94 | 0.89 | 1.00 | 0.92 | 0.94 | 0.89 |
| RF00581 | 0.94 | 0.89 | 1.00 | 0.94 | 0.89 | 1.00 | 1.00 | 1.00 | 1.00 | 0.94 | 0.89 | 1.00 |
| RF00238 | 1.00 | 1.00 | 1.00 | N/A | N/A | N/A | 0.91 | 0.83 | 1.00 | 0.89 | 0.83 | 0.95 |
| RF00477 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
| RF00608 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| RF00468 | 0.65 | 0.65 | 0.65 | N/A | N/A | N/A | 0.94 | 0.94 | 0.94 | 0.65 | 0.65 | 0.65 |
| RF00489 | 0.96 | 0.92 | 1.00 | 0.92 | 0.85 | 1.00 | 0.96 | 0.92 | 1.00 | 0.96 | 0.92 | 1.00 |
| RF00113 | 0.85 | 0.83 | 0.87 | 0.79 | 0.79 | 0.79 | 0.98 | 0.96 | 1.00 | 0.98 | 0.96 | 1.00 |
|
| ||||||||||||
| Mean | 0.86 | 0.83 | 0.89 | 0.88 | 0.84 | 0.94 | 0.89 | 0.85 | 0.93 | 0.94 | 0.92 | 0.96 |
| Std. Dev. | 0.24 | 0.25 | 0.24 | 0.15 | 0.18 | 0.12 | 0.23 | 0.24 | 0.23 | 0.08 | 0.09 | 0.08 |
The best MCC value for each family, and the best mean and standard deviation are highlighted in bold. Note that RSpredict has the best standard deviation in MCC, SN and SL respectively compared with the other three tools. This shows that RSpredict has stable performance across all the families tested in the experiment.