Table 8 Comparison of accuracy as measured by F-measure for KnotAli with RNAalifold, Hxmatch, and Cacofold when compatible bases are not considered as false positive
From: KnotAli: informed energy minimization through the use of evolutionary information
Family | MUSCLE | MAFFT | ||||||
|---|---|---|---|---|---|---|---|---|
KnotAli | RNAalifold | Hxmatch | Cacofold | KnotAli | RNAalifold | Hxmatch | Cacofold | |
5s | .920 | .840 | .581 | .886 | .922 | .765 | .550 | .832 |
16s | .560 | .635 | .527 | .267 | .593 | .677 | .588 | .297 |
23s | .639 | .851 | .652 | .318 | .401 | .851 | .657 | .314 |
Group I intron | .549 | .087 | .065 | .079 | .474 | .069 | .068 | .093 |
Group II intron | .205 | 0 | .018 | 0 | .431 | .189 | .182 | .186 |
RNaseP | .547 | .341 | .225 | .255 | .645 | .322 | .123 | .415 |
SRP | .620 | .250 | .250 | .264 | .463 | .135 | .135 | .218 |
Telomerase | .336 | .610 | .430 | .479 | .278 | .325 | .361 | .533 |
tmRNA | .556 | .395 | .294 | .372 | .578 | .319 | .087 | .373 |
tRNA | .961 | .951 | .854 | .926 | .917 | .858 | .760 | .885 |