Timing of BLAT vs.WU-TBLASTX on a Data Set of 1000 Mouse Reads and a RepeatMasked Human Chromosome 22
| Method | K | N | Matrix | Time |
| WU-TBLASTX | 5 | 1 | +15/−12 | 2736 s |
| WU-TBLASTX | 5 | 1 | BLOSUM62 | 2714 s |
| BLAT | 5 | 1 | +2/−1 | 61 s |
| BLAT | 4 | 2 | +2/−1 | 37 s |
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The first WU-TBLASTX run was performed using the settings used in Exofish. The second WU-TBLASTX run was performed using the settings B = 9000 V = 9000 hspmax = 4 topcomboN = 1 W = 5 E = 0.01 Z = 3000000000 nogaps filter = xnu + seg. The K column indicates the size of the perfectly matching hit that serves as a seed for an alignment. The N column indicates how many hits in a gapless 100-amino acid window were required to trigger a detailed alignment. The Matrix column describes the match/mismatch scores or the substitution score matrix used.
