Table 2.

Percentage of matched genes in self-aligned networks reported for MAGNA++, IsoRankN, and Juxtapose

	MAGNA++				IsoRankN				Juxtapose
	alpha 0.50	alpha 0.95	alpha 0.50 with 50% bitscores	alpha 0.50 with 100% bitscores	alpha 0.50	alpha 0.95	alpha 0.50 with 50% bitscores	alpha 0.50 with 100% bitscores	N/A
Line	0	0.10	0.52	1.0	0.24	0.19	0.0	1.0	1.0
Circle	0	0.14	0.57	1.0	0.33	0.29	0.0	1.0	1.0
Cross	0.24	0.02	0.52	1.0	0.29	0.19	0.83	1.0	1.0
Heart	0.93	0.93	0.99	1.0	0.16	0.04	0.71	1.0	1.0
Brain	0.33	0.55	0.99	1.0	0.18	0.07	0.82	1.0	1.0

The alpha values indicate the balance between node similarity and edge similarity (MAGNA++) or the balance between topological similarity and sequence similarity (IsoRankN). When no percentage of bitscores is provided, the algorithm was not provided with informative bitscores i.e. the match between any genes was equally likely. When 50% of bitscores were provided, 50% of the genes had the highest bitscore provided for the real match between the genes of both networks. When 100% of bitscores were provided, 100% of the genes had the highest bitscore provided for the real match between the genes of both networks. N/A is given for the settings in Juxtapose as no bitscore file is provided and no alpha value is provided to the tool