Table 6.
Best methods according to rankings on the RNAstrand data set
| Ranking type | First rank | Second rank | Third rank | |
|---|---|---|---|---|
| All RNAs | ext | TurboFold(seed) (W: 52, L: 1, NW: 0) | TurboFold(20) (W: 51, L: 1, NW: 1) | ContextFold (W: 51, L: 2, NW: 0) |
| Short RNAs (20–200 nt) | ext | ContextFold (W: 53, L: 0, NW: 0) | TurboFold(20) (W: 51, L: 1, NW: 1) | CentroidHomfold-LAST and CentroidAlifold(seed) (W: 50, L: 3, NW: 0) |
| Medium-sized RNAs (201–800 nt) | ext | ContextFold (W: 43, L: 3, NW: 7) | CentroidAlifold(seed) (W: 42, L: 4, NW: 7) | TurboFold(20) (W: 40, L: 1, NW: 12) |
| Long RNAs (801–30 000 nt) | ext | ContextFold (W: 24, L: 0, NW: 29) | CentroidAlifold(seed) and CentroidAlifold(20) (W: 22, L: 1, NW: 30) | RNAalifold(seed)a (W: 21, L: 3, NW: 29) |
| All pseudoknotted RNAs | ext | CentroidAlifold(seed) (W: 46, L: 4, NW: 3) | ContextFold (W: 45, L: 5, NW: 3) | CentroidHomfold-LAST (W: 43, L: 8, NW: 2) |
| Pseudoknotted-short RNAs (20–200 nt) | ext | Cylofold (W: 35, L: 0, NW: 18) | McQFold (W: 35, L: 1, NW: 17) | Pknots (W: 33, L: 2, NW: 18) |
| Pseudoknotted medium-sized RNAs (201–800 nt) | ext | ContextFold (W: 42, L: 0, NW: 11) | TurboFold(20) (W: 39, L: 1, NW: 13) | PPfold(20) (W: 38, L: 2, NW: 13) |
| Pseudoknotted long RNAs (801–30 000 nt) | ext | ContextFold (W: 24, L: 0, NW: 29) | CentroidAlifold(seed) and CentroidAlifold(20) (W: 22, L: 1, NW: 30) | RNAalifold(seed)a (W: 21, L: 3, NW: 29) |
| Robustness test—1987 sequences | ext | ContextFold (W: 53, L: 0, NW: 0) | IPknot (W: 52, L: 1, NW: 0) | Contrafold (W: 51, L: 2, NW: 0) |
| Robustness test—1242 sequences with Rfam family assigned | ext | ContextFold (W: 53, L: 0, NW: 0) | CentroidAlifold(seed) (W: 52, L: 1, NW: 0) | IPknot (W: 51, L: 2, NW: 0) |
aFourth place.
W = number of wins; L = number of defeats; NW = number of cases in which it was impossible to select winner; (20) = refers to the test of a comparative method in which 20 representatives of an Rfam seed alignment were used; (seed) = refers to the test in which all sequences from a given seed alignment were used.