Table 3.
Running time in seconds for baseline and indexed versions of MegaBLAST in the case of the unmasked human genome database
| Set | <5000 results |
≥5000 results |
||||
|---|---|---|---|---|---|---|
| Count | Baseline | Indexed | Count | Baseline | Indexed | |
| Qlarge | 1 | 5.08 | 3.49 | 61 | 44173.96 | 43888.14 |
| 1.46 | 0.29 | 961.24 | 1396.93 | |||
| Qmedium | 13 | 82.17 | 71.95 | 87 | 13009.04 | 13325.62 |
| 24.06 | 6.29 | 305.10 | 745.59 | |||
| Qsmall | 88 | 118.05 | 56.51 | 12 | 528.85 | 570.84 |
| 68.19 | 7.24 | 13.70 | 65.86 | |||
For each query set the top row contains the number of queries in the corresponding group and the total search time. The second row shows the time taken by the seed search phase only. For 38 queries in Qlarge, at least one version of MegaBLAST ran out of memory due to the large number of results.