Table 1.

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

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.