General performance of SEA incorporating different local structure diversities

subset	measures	CE	SEA_true	SEA_c30	SEA_c10	SEA_c5	SEA_1d	BLAST	ALIGN	FFAS
Family (409 pairs)	average-shift		0.61	0.56	0.56	0.54	0.49	0.44	0.48	0.49
	shift>0.9		73	69	63	56	47	51	60	43
	shift>0.7		207	199	192	183	152	146	165	161
	shift>0.5		282	260	259	251	215	197	228	227
	RMSD£3.0	257	95	82	82	76	63	77	54	40
	RMSD£5.0	397	237	184	171	177	147	157	138	118
	RMSD£8.0	408	294	248	249	249	231	196	206	194
	all	409	345	404	398	368	366	232	372	409
Superfamily (225 pairs)	average-shift		0.27	0.12	0.12	0.12	0.08	0.09	0.06	0.07
	shift>0.9		3	3	3	2	0	1	2	1
	shift>0.7		17	8	9	7	4	10	9	7
	shift>0.5		54	26	23	21	17	18	18	17
	RMSD£3.0	55	12	6	6	7	6	8	3	1
	RMSD£5.0	160	44	16	18	18	11	18	11	1
	RMSD£8.0	163	69	37	34	41	28	23	22	15
	all	166	128	217	204	181	177	41	149	225

Two subsets of the benchmark (family-level subset and superfamily-level subset) are compared with SEA_c30, SEA_c10, SEA_c5, SEA_true, SEA_1d, and other programs: CE (structural alignment), BLAST, ALIGN and FFAS (profile-profile alignment). The alignment quality is evaluated by the shift score and RMSD. The average-shift row lists the shift score averaged over all the alignments of the each subset by different programs. The number of alignments with shift score > 0.9, > 0.7 and > 0.5, RMSD £ 3.0, £ 5.0 and £ 8.0 in each subset are also listed in rows. The counting according to RMSD requires the length of the alignment is no short than half of its corresponding structural alignment. The all row lists the number of alignments with alignment length no short than half of the structural alignments in each subset. As the structural alignments from CE are used as reference alignments for shift score calculation, its evaluation by shift score is meaningless and the corresponding numbers are blanked out.