Table 1.
Performance runtime comparison (in s) between PHAST, PHASTER and PHASTEST using identical (new) hardware, but with different databases, search algorithms and query types using E. coli O157:H7 (NC_002655.2) as the query genome
| Cumulative set of performance enhancements | BLAST vs. phage database runtime (sec) | BLAST vs. bacterial database runtime (sec) | GenBank annotated genome runtime (sec) | Unannotated genome runtime (sec) |
|---|---|---|---|---|
| PHAST (baseline) - current DBs, no other upgrades | 191 | 576 | 270 | 899 |
| PHASTER (baseline) - current DBs, no other upgrades | 116 | 83 | 162 | 277 |
| PHASTEST (upgrade 1) - BLAST+ parameter adjustment | 82 | 82 | 144 | 229 |
| PHASTEST (upgrade 2) - Whole-sequence Prodigal | 81 | 71 | 141 | 201 |
| PHASTEST (upgrade 3) - Parallel Diamond | 84 | 124 | 118 | 266 |
| PHASTEST (upgrade 4) - Swiss-Prot DB | 80 | 64 | 110 | 195 |