Table 4.
Running time in seconds for baseline and indexed versions of MegaBLAST in the case of masked genomes and query masked (indicated by yes) or unmasked (indicated by no)
| Human masked |
Mouse masked |
|||||
|---|---|---|---|---|---|---|
| Set | Baseline | Indexed |
Baseline | Indexed |
||
| Yes | Yes | No | Yes | Yes | No | |
| Qlarge | 1097.11 | 511.76 | 418.31 | 1702.35 | 736.74 | 613.17 |
| 447.42 | 108.32 | 127.60 | 447.50 | 98.71 | 114.07 | |
| Qmedium | 266.43 | 90.80 | 95.36 | 437.45 | 146.63 | 140.94 |
| 176.21 | 23.97 | 28.64 | 162.15 | 22.82 | 25.63 | |
| Qsmall | 104.79 | 27.24 | 26.44 | 148.98 | 64.93 | 67.76 |
| 76.83 | 5.27 | 5.33 | 70.10 | 5.32 | 5.11 | |
| Quser | 144.06 | 46.12 | NA | 164.21 | 82.82 | NA |
| 93.49 | 8.27 | NA | 83.18 | 7.01 | NA | |
For each query set the top row is the total search time, and the second row is the time taken for the seed search phase only. NA—not applicable.