Table 1.

Summary of sequence comparison methods with pdb40d-b

Method	Relative Time*	1% EPQ Cutoff	Coverage at 1% EPQ
ssearch % identity: within alignment	25.5	>70%	<0.1
ssearch % identity: within both	25.5	34%	3.0
ssearch % identity: hssp-scaled	25.5	35% (hssp + 9.8)	4.0
ssearch Smith–Waterman raw scores	25.5	142	10.5
ssearch E-values	25.5	0.03	18.4
fasta ktup = 1 E-values	3.9	0.03	17.9
fasta ktup = 2 E-values	1.4	0.03	16.7
wu-blast2 P-values	1.1	0.003	17.5
blast P-values	1.0	0.00016	14.8

^*Times are from large database searches with genome proteins.