Table 4 Comparison of RNAalifold with and without the use of RIBOSUM matrices as a covariation measure
From: KnotAli: informed energy minimization through the use of evolutionary information
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* |