Table 3.
Computation time for calculating base-pairing probabilities of sequences of various lengths.
| ID | PKB229 | PKB134 | ASE_00193 | CRW_00614 | CRW_00774 |
|---|---|---|---|---|---|
| Length (nt) | 67 | 137 | 301 | 494 | 989 |
| Neuralfold (FNN) IPknot |
3.30 s | 27.78 s | 44.73 s | 60.22 s | 3 m 4.2 s |
| (w/o refine.) | 0.01 s | 0.05 s | 0.18 s | 0.55 s | 2.64 s |
| (w/refine.) | 0.03 s | 0.08 s | 0.31 s | 1.03 s | 5.86 s |
| (D&P) | 8.36 s | 9 m 4.7 s | n/a | n/a | n/a |
Computation time was measured on an Intel Xeon E5-2680 (2.80 GHz) computer with 64 GB of memory and running Linux OS v2.6.32. FNN, feedforward neural network; D&P, Dirks–Pierce. IPknot with D&P failed to compute due to lack of memory for sequence lengths greater than 300.