Table 1.

Pairwise alignment results for the IsoBase dataset. Protein functionality is determined based on the KEGG Orthology (KO) group annotations

	Yeast – Fly		Yeast – Worm		Yeast – Human		Yeast – Mouse		Fly – Worm
	CN a	SPE b	CN	SPE	CN	SPE	CN	SPE	CN	SPE
CUFID-align	1,708	0.748	1,548	0.834	1,330	0.736	1,304	0.794	2,616	0.873
SMETANA-CSRW	1,610	0.757	1,426	0.850	1,224	0.733	1,192	0.802	2,444	0.870
SMETANA	1,530	0.733	1,422	0.843	1,134	0.710	1,182	0.782	2,338	0.852
PINALOG	1,368	0.722	640	0.737	1,100	0.682	76	0.400	672	0.689
HubAlign	1,326	0.681	98	0.170	1,082	0.633	42	0.231	102	0.201
IsoRank	1,414	0.712	650	0.703	1,142	0.702	76	0.369	918	0.818
BLAST-MWBMc	1,712	0.776	1,544	0.836	1,334	0.768	1,280	0.792	2,680	0.885
	Fly – Human		Fly – Mouse		Worm – Mouse		Worm – Human		Human – Mouse
	CN	SPE	CN	SPE	CN	SPE	CN	SPE	CN	SPE
CUFID-align	2,528	0.754	2,364	0.788	1,818	0.807	1,858	0.791	5,178	0.983
SMETANA-CSRW	2,358	0.763	2,146	0.768	1,610	0.811	1,722	0.803	5,002	0.978
SMETANA	2,096	0.706	2,112	0.764	1,578	0.803	1,570	0.780	4,876	0.972
PINALOG	1,172	0.604	118	0.567	66	0.458	482	0.677	282	0.972
HubAlign	354	0.219	34	0.230	24	0.188	32	0.063	144	0.667
IsoRank	1,736	0.725	146	0.566	72	0.456	644	0.793	286	0.979
BLAST-MWBM	2,580	0.766	2,374	0.781	1,824	0.808	1,884	0.794	5,140	0.982

^aCN: ccorrect nodes

^bSPE: specificity

^cBLAST-MWBM: maximum weighted bipartite matching of PPI networks only using the BLAST bit score

In each column, the best performance is shown in boldface