Table 3.
The results of the run time evaluation on partial human lncRNA and mRNA datasets
| The number of lncRNAs and mRNAs | |||||
|---|---|---|---|---|---|
| Program | 5 × 5 | 10 × 10 | 50 × 50 | 100 × 100 | 500 × 500 |
| IntaRNA | 59 m 04 s (126.6) | 3 h 30 m 17 s (252.3) | − (-) | − (-) | − (-) |
| RNAplex-a | 2 m 34 s (5.5) | 10 m 37 s (12.8) | 4 h 20 m 42 s (47.0) | 17 h 56 m (63.4) | 19 d 20 h 53 m (74.1) |
| Terai et al. pipeline | 1 m 02 s (2.2) | 3 m 08 s (3.8) | 2 h 26 m 43 s (26.4) | 14 h 50 m (52.4) | 17 d 09 h 44 m (64.9) |
| RIblast | 28 s (1.0) | 50 s (1.0) | 5 m 33 s (1.0) | 17 m (1.0) | 6 h 26 m (1.0) |
Note: The columns correspond to the number of lncRNAs assessed in the dataset. The rows indicate the run times and the run time ratio of each program to RIblast. The symbol ‘−’ indicates that we did not investigate the computational speed for a particular combination of dataset size and program because the calculation time was prohibitively long.