An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Table 5

Running times of the programs on 3 data sets of yeast protein interactions on a Pentium IV 3.0 GHz processor with 512 MB memory.

Program	MIPS data (4874 nodes 15660 edges)	DIP data (4932 nodes 17491 edges)	BOND data (18692 nodes 59516 edges)
Our program	10.06 s	13.06 s	1 m 06.63 s
CFinder	17.45 s	24.33 s	2 m 22.46 s

MIPS data: PPI_180105.tab from MIPS (1/18/2005).
DIP data: yeast20071104.lst from DIP (11/04/2007).
BOND data: data from BOND (11/9/2007).