Predicting direct protein interactions from affinity purification mass spectrometry data

Table 5 Running times of the algorithm

Network	(i) 1-cut & degree 2 vertices (secs)	(ii) Quasi-clique predictions	(iii) Genetic algorithm
Yu	0:00:29	0:31:02	15:00:00
DIP	0:00:41	0:48:14	15:00:00
PAM	0:00:19	0:29:49	15:00:00
DM	0:00:24	1:18:03	15:00:00

Running times of our method on the model networks for each phase of the algorithm: (i) detecting 1-cut vertices and degree two vertices; (ii) predicting quasi-clique clusters; and (iii) running the genetic algorithm. We are reporting the average run time over three runs on each network. The implementation was tested on a Powermac G5 2 Ghz with 4 GB of RAM. Note that the genetic algorithm was run for a fixed amount of time, and the top scoring candidates achieved the quality as shown in Table 3. The times are shown in hh.mm.ss format.