Table 2.

Running time. The running time (in seconds) to perform all pairwise comparisons of 5,345 domains for the SSEF, LFF, SGM, and PRIDE2 methods. The running time is broken into running times spent on the pre-processing step and the distance computation step. The pre-processing step includes all the computation necessary to compute projections for 5, 345 domains. The distance computation step includes all pairwise distance computations between 5,345 projections computed in the pre-processing step. As the detailed information is not available for the PRIDE2 method, only the total time is shown for this method.

	Running time in seconds
	ssef	lff	sgm	pride
pre-processing	3,067	490, 449	4,397	not available
distance computations	1,054	169	136	not available
total	4,121	490, 618	4,533	13, 200