Table 4. Query times for various variants of indexes for simulated data.
|
sparsity | size | Max. allowed mismatches | |||||
| [GB] | 0 | 1 | 2 | 3 | 4 | 5 | ||
| 25 | 1 | 24.7 | 214.2 | 450.8 | 699.5 | 971.5 | 1,438.3 | 2,976.8 |
| 25 | 3 | 11.8 | 225.0 | 481.2 | 751.6 | 1,024.3 | 1,599.9 | 3,647.1 |
| 25 | 4 | 10.2 | 229.8 | 493.1 | 754.0 | 1,050.9 | 1,676.4 | 4,004.2 |
| 25 | 8 | 7.7 | 243.1 | 528.3 | 814.6 | 1,158.5 | 2,341.4 | 6,790.4 |
| 25 | 12 | 6.9 | 257.2 | 558.3 | 868.0 | 1,337.8 | ||
| 25 | 16 | 6.5 | 268.8 | 588.6 | 916.6 | 1,787.9 | ||
| 30 | 1 | 26.3 | 85.4 | 193.4 | 303.0 | 456.0 | 1,036.4 | 3,004.6 |
| 30 | 3 | 12.3 | 95.7 | 220.8 | 340.6 | 520.4 | 1,258.0 | 3,716.2 |
| 30 | 4 | 10.6 | 100.4 | 227.8 | 351.5 | 544.0 | 1,376.5 | 4,104.5 |
| 30 | 8 | 7.9 | 121.8 | 267.0 | 414.5 | 713.6 | 2,215.2 | 6,994.5 |
| 30 | 12 | 7.1 | 134.0 | 291.4 | 456.4 | 959.4 | ||
| 30 | 16 | 6.6 | 149.2 | 319.3 | 506.8 | 1,490.4 | ||
| 35 | 1 | 27.9 | 41.4 | 98.0 | 152.0 | 301.8 | 1,033.4 | 3,114.6 |
| 35 | 3 | 12.9 | 53.6 | 121.2 | 193.0 | 380.4 | 1,280.8 | 3,861.2 |
| 35 | 4 | 11.0 | 58.6 | 130.2 | 206.3 | 419.2 | 1,411.7 | 4,277.6 |
| 35 | 8 | 8.2 | 77.2 | 166.1 | 260.3 | 608.3 | 2,224.4 | 7,120.4 |
| 35 | 12 | 7.2 | 93.3 | 196.2 | 314.6 | 905.3 | ||
| 35 | 16 | 6.8 | 107.0 | 222.2 | 382.4 | 1,506.4 | ||
| 40 | 1 | 29.6 | 28.8 | 65.2 | 102.3 | 291.0 | 1,109.9 | 3,348.8 |
| 40 | 3 | 13.4 | 39.4 | 85.5 | 136.1 | 372.5 | 1,334.0 | 4,021.0 |
| 40 | 4 | 11.4 | 43.4 | 94.4 | 151.4 | 412.2 | 1,471.1 | 4,461.1 |
| 40 | 8 | 8.4 | 61.0 | 128.9 | 210.3 | 615.4 | 2,297.9 | 7,350.3 |
| 40 | 12 | 7.4 | 76.3 | 160.0 | 271.8 | 917.0 | ||
| 40 | 16 | 6.9 | 90.4 | 184.4 | 344.3 | 1,514.1 | ||
| 45 | 2 | 18.3 | 25.9 | 56.2 | 97.9 | 329.6 | 1,207.0 | 3,687.2 |
| 45 | 3 | 14.0 | 31.3 | 67.7 | 116.5 | 375.5 | 1,353.3 | 4,115.0 |
| 45 | 4 | 11.8 | 36.3 | 77.2 | 132.6 | 421.2 | 1,490.9 | 4,525.3 |
| 45 | 8 | 8.6 | 54.2 | 112.4 | 196.2 | 625.8 | 2,394.4 | 7,523.9 |
| 45 | 12 | 7.5 | 70.4 | 142.9 | 262.5 | 942.0 | ||
| 45 | 16 | 7.0 | 82.1 | 168.4 | 342.3 | 1,531.9 | ||
| GEM mapper | 5.0 | 24.0 | 50.6 | 64.9 | 86.4 | 131.0 | 217.3 | |
All times in µs. We do not provide times for large sparsities and more errors than 3, since in such cases the internal queries would be for very short sequences and in turn result in numerous matches and significant times; thus, we do not recommend to use MuGI in such parameter configurations.