Table 1 Clustering calculation time for each method with datasets of different sizes. Sequences (≥ 10) and sequences (≥ 100) represent filtered data with frequency cutoff. DNF indicates did not finish. DNF 1: FASTAptamer did not complete the calculation for the entire sequence dataset in 7 days. DNF 2: APTANI showed a calculation error after the prediction of the secondary structure, which took 25 h
|  | All sequences |  | Sequences (≥ 10) |  | Sequences (≥ 100) |  |
|---|---|---|---|---|---|---|
Method | Real time | CPU time | Real time | CPU time | Real time | CPU time |
FASTAptamer | DNF 1 | DNF 1 | 5 h 16 m 4 s | 5 h 16 m 3 s | 10 m 40 s | 10 m 40 s |
AptaCluster | 3 m 45 s | 4 m 9 s | 33 s | 26 s | 28 s | 17 s |
APTANI | DNF 2 | DNF 2 | 32 m 52 | 34 m 59 s | 1 m 47 s | 1 m 20 s |
AptaTRACE | 71 h 38 m 35 s | 246 h 15 m 12 s | 1 h 1 m 17 s | 2 h 2 m 50 s | 3 m 52 s | 5 m 44 s |
FSBC | 4 h 40 m 51 s | 4 h 40 m34 s | 9 m 25 s | 9 m 17 s | 51 s | 46 s |