From: KnotAli: informed energy minimization through the use of evolutionary information
Family | KnotAli | RNAalifold | Hxmatch | Cacofold | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sen | ppv | F | Sen | ppv | F | Sen | ppv | F | Sen | ppv | F | |
(a) Input alignment created through MUSCLE | ||||||||||||
5s | .899 | .876 | .887 | .761 | .884 | .817 | .424 | .917 | .579 | .835 | .859 | .846 |
16s | .494 | .501 | .494 | .506 | .748 | .602 | .385 | .724 | .502 | .172 | .455 | .250 |
23s | .589 | .545 | .566 | .798 | .767 | .782 | .552 | .625 | .587 | .242 | .341 | .283 |
Group I intron | .490 | .444 | .461 | .047 | .588 | .087 | .034 | .529 | .064 | .039 | .300 | .068 |
Group II intron | .177 | .139 | .154 | 0 | 0 | 0 | .010 | .108 | .018 | 0 | 0 | 0 |
RNaseP | .498 | .491 | .493 | .235 | .602 | .334 | .135 | .699 | .225 | .164 | .552 | .251 |
SRP | .580 | .556 | .564 | .165 | .764 | .241 | .166 | .897 | .25 | .186 | .496 | .255 |
Telomerase | .289 | .233 | .256 | .508 | .636 | .563 | .292 | .711 | .413 | .380 | .480 | .423 |
tmRNA | .491 | .468 | .477 | .255 | .803 | .386 | .176 | .852 | .291 | .234 | .868 | .367 |
tRNA | .950 | .917 | .932 | .931 | .972 | .949 | .764 | .974 | .854 | .886 | .970 | .925 |
(b) Input alignment created through MAFFT | ||||||||||||
5s | .902 | .871 | .885 | .644 | .843 | .729 | .385 | .927 | .541 | .739 | .852 | .790 |
16s | .548 | .495 | .519 | .548 | .794 | .647 | .440 | .802 | .567 | .198 | .467 | .277 |
23s | .329 | .468 | .361 | .795 | .771 | .783 | .563 | .627 | .593 | .281 | .336 | .281 |
Group I intron | .424 | .378 | .396 | .036 | .719 | .068 | .036 | .719 | .069 | .051 | .384 | .090 |
Group II intron | .382 | .244 | .295 | .106 | .773 | .186 | .103 | .580 | .175 | .105 | .920 | .187 |
RNaseP | .592 | .583 | .585 | .207 | .759 | .322 | .067 | .700 | .122 | .301 | .639 | .400 |
SRP | .420 | .416 | .415 | .078 | .661 | .129 | .078 | .885 | .134 | .148 | .377 | .206 |
Telomerase | .243 | .186 | .211 | .25 | .361 | .294 | .255 | .483 | .333 | .442 | .517 | .475 |
tmRNA | .504 | .492 | .495 | .196 | .799 | .313 | .047 | .435 | .084 | .255 | .650 | .362 |
tRNA | .898 | .878 | .886 | .8 | .931 | .855 | .642 | .940 | .758 | .853 | .925 | .882* |