Table 1.

mBed performance on the ten biggest Pfam/HOMSTRAD families.

Name	Size	Len	%ID	Embedding Time (s)					Distance Matrix Calculation Time (s)					Alignment Column Score (%)
					(1)	(2)	(3)	(4)		(1)	(2)	(3)	(4)		(1)	(2)	(3)	(4)
PF01381	9993	53	23		-	25	55	136		764	57	55	175		13.3	26.7	25.3	34.7
PF00006	9796	209	43		-	134	248	280		4364	48	49	88		42.8	36.6	36.6	38.0
PF00989	9681	95	17		-	43	88	197		1281	50	51	159		46.5	33.3	31.8	34.1
PF00486	9615	75	30		-	34	69	107		950	55	52	104		63.9	92.8	64.9	89.7
PF00571	9551	119	19		-	73	143	268		1993	54	50	152		6.15	3.08	1.54	1.54
PF00097	9423	41	33		-	18	38	94		517	44	43	115		53.2	54.8	61.3	54.8
PF01479	9352	47	32		-	17	40	90		496	45	46	124		58.3	91.7	89.6	79.2
PF00046	9305	54	35		-	20	43	85		651	41	42	77		59.4	44.9	46.4	60.9
PF00550	9249	63	25		-	28	59	136		794	47	47	141		51.3	32.9	55.3	59.2
PF00149	9072	198	14		-	133	256	552		3515	47	46	172		75.4	71.9	72.3	76.1
Average	9503	95	27		0	53	104	195		1533	49	48	131		47.0	48.9	48.5	52.8

The ten biggest Pfam entries containing 9,000-10,000 sequences, which have a corresponding HOMSTRAD alignment are used here. Four different methods were applied to each entry to calculate a distance matrix. These methods are: (1) the traditional process of calculating a full distance matrix from the sequence data using an alignment distance measure; (2) mBed default; (3) mBed followed by the 'usePivotObjects' method; (4) mBed followed by the 'usePivotGroups' method. A UPGMA guide tree is constructed from each matrix and used as a guide tree for progressive alignment of the sequences. The alignment is then scored against the corresponding HOMSTRAD structural alignment using Column Score.

(1) Full d(x, y) distance matrix; (2) mBed; (3) mBed + usePivotObjects; (4) mBed + usePivotGroups