Table 1.

Summary of results from all methods used (human network)

	Sequence-based alignment	Function-based alignment	Combined method	MaWISH	Network blast	Combined method 3-way	Simultaneous clustering	GO clustering
Number of clusters	74	94	303	242	2353	430	1197	1093
Number of proteins	457	727	1479	543	894	1603	7371	6663
MIPS coverage	96	126	283	83	153	327	424	346
MIPS accuracy	0.18	0.24	0.21	0.1	0.08	0.17	0.05	0.03
Functional coherence	0.36	0.51	0.43	0.32	0.3	0.40	0.23	0.29
Run time (s)	3061	5432	21	663	68 977	29	369	112