Table 4.
Comparison of RNAalifold with and without the use of RIBOSUM matrices as a covariation measure
| Family | MUSCLE | MAFFT | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RNAalifold | Riboalifold | RNAalifold | Riboalifold | |||||||||
| Sen | ppv | F | Sen | ppv | F | Sen | ppv | F | Sen | ppv | F | |
| 5s | .561 | .929 | .698 | .761 | .884 | .817 | .419 | .979 | .586 | .644 | .843 | .729 |
| 16s | .323 | .818 | .462 | .505 | .748 | .602 | .336 | .852 | .481 | .548 | .794 | .647 |
| 23s | .805 | .815 | .81 | .798 | .767 | .782 | .807 | .806 | .807 | .895 | .771 | .783 |
| Group I intron | 0 | 0 | 0 | .047 | .588 | .087 | 0 | 0 | 0 | .036 | .719 | .068 |
| Group II intron | 0 | 0 | 0 | 0 | 0 | 0 | .105 | .992 | .189 | .106 | .773 | .186 |
| RNaseP | 0 | 0 | 0 | .235 | .602 | .334 | 0 | 0 | 0 | .207 | .759 | .322 |
| SRP | .124 | .897 | .198 | .165 | .764 | .241 | .079 | .883 | .135 | .078 | .661 | .129 |
| Telomerase | .223 | .793 | .348 | .508 | .636 | .563 | .225 | .869 | .356 | .25 | .361 | .294 |
| tmRNA | .147 | .978 | .254 | .255 | .803 | .386 | .123 | .955 | .216 | .196 | .799 | .313 |
| tRNA | .857 | .973 | .909 | .931 | .972 | .949 | .757 | .93 | .829 | .8 | .931 | .855* |
RNAalifold refers to RNAalifold with Hamming distance (default) and Riboalifold is used to denote RNAalifold with RIBOSUM matrices. Results are shown across both MUSCLE and MAFFT. BOLD is used to show significant difference in the results. An * is added when the significance is close enough to warrant distinction but not fully crossing a p-value of .05