Global multiple protein-protein interaction network alignment by combining pairwise network alignments

BMC Bioinformatics

Table 3 Performance of SMAL

max-scores (SMAL)	NA	NF	NH	NForH	EA-2	EA	EF	EH	EForH
IsoRankN first	Human 64812	Mouse 22464	Human 4676	Mouse 23598	Human 1665	Yeast 68329	Arabi 27733	Arabi 749	Arabi 28031
IsoRankN second	Celeg 62677	Human 21849	Mouse 4459	Human 23090	Yeast 1458	Arabi 66757	Human 9038	Human 380	Human 9107
SMETANA first	Human 349645	Human 165645	Celeg 19876	Human 170367	Human 5328	Human 1038837	Arabi 809249	Arabi 5420	Arabi 809594
SMETANA second	Droso 313439	Droso 139636	Human 16432	Droso 144107	Yeast 3741	Arabi 1020591	Human 268958	Human 4155	Human 269553
PINALOG first	Human 35996	Human 12093	Human 6873	Human 13930	Yeast 8541	Yeast 12174	Human 1509	Human 971	Human 1815
PINALOG second	Yeast 35970	Droso 11325	Mouse 5217	Droso 12749	Human 7387	Human 10560	Yeast 1347	Yeast 644	Yeast 1595
NETAL first	Droso 67555	Human 1523	Droso 7	Human 1526	Human 21947	Human 63412	Human 173	Droso, Human 1	Human 174
NETAL second	Human 66700	Droso 1437	Human 5	Droso 1440	Droso 14318	Droso 39302	Droso 56	-, 0	Droso 57

For a given algorithm and measure, the scaffold PPIN with the highest and second highest score obtained through SMAL MNA is presented, along with the achieved score. For easy comparison with Table 2, the species with highest and second highest pairwise sum score are bold and underlined, respectively. For every measure and algorithm tested, the highest scoring species from Table 2 is always either the highest or second highest scoring species in Table 3 (this table), demonstrating measure consistency of SMAL and validating the proposed scaffold selection strategy.

ISSN: 1471-2105