LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules

BMC Genomics

Table 1 Comparison of local network alignment results of three previous algorithms and the proposed method and their f-scores as prediction accuracy of conserved protein complexes

	Human-yeast network alignment				Human-fruit fly network alignment				Yeast-fruit fly network alignment
	Num. of clusters		f-score		Num. of clusters		f-score		Num. of clusters		f-score
Algorithms	Human	Yeast	Human	Yeast	Human	Fruit fly	Human	Fruit fly	Yeast	Fruit fly	Yeast	Fruit fly
NetworkBlast	1626	1695	0.431	0.428	1162	925	0.348	0.174	70	65	0.411	0.315
AlignMCL	926	838	0.285	0.285	683	681	0.279	0.161	309	309	0.279	0.176
LocalAli	400	400	0.164	0.172	400	400	0.170	0.121	384	384	0.171	0.133
LePrimAlign	180	175	0.418	0.441	201	179	0.430	0.253	110	105	0.352	0.235

Three different pairs of PPI networks have been aligned: the human and yeast PPI network pair, the human and fruit fly PPI network pair, and the yeast and fruit fly PPI network pair

ISSN: 1471-2164