Request ID: 00513

Table 1. High Resolution Accuracy

Table 2. Low Resolution Accuracy

Table 3. Confusion with Globular Proteins

Table 4. Confusion with Signal Peptides

Table 1. High Resolution Accuracy (Sorting on column 1 - highlighted)

	Per-segment accuracy			Per-residue accuracy
Method ?	Qok ?	Qhtm %obs ?	Qhtm %prd ?	Q2 ?	Q2T %obs ?	Q2T %prd ?	Q2N %obs ?	Q2N %prd ?
PHDpsihtm08	84	99	98	80	76	83	86	80
HMMTOP2	83	99	99	80	69	89	88	71
DAS	79	99	96	72	48	94	96	62
TopPred2	75	90	90	77	64	83	90	69
TMHMM1	71	90	90	80	68	81	89	72
SOSUI	71	88	86	75	66	74	80	69
PHDhtm07	69	83	81	78	76	82	84	79
KD	65	94	89	67	79	66	52	67
PHDhtm08	64	77	76	78	76	82	84	79
GES	64	97	90	71	74	72	66	69
PRED-TMR	61	84	90	76	58	85	94	66
Ben-Tal	60	79	89	72	53	80	95	63
Eisenberg	58	95	89	69	77	68	57	68
Hopp-Woods	56	93	86	62	80	61	43	67
WW	54	95	91	71	71	72	67	67
Roseman	52	94	83	58	83	58	34	66
Av-Cid	52	93	83	60	83	58	39	72
Levitt	48	91	84	59	80	58	38	67
A-Cid	47	95	83	58	80	56	37	66
Heijne	45	93	82	61	85	58	34	64
Bull-Breese	45	92	82	55	85	55	27	66
Sweet	43	90	83	63	83	60	43	69
Radzicka	40	93	79	56	85	55	26	63
Nakashima	39	88	83	60	84	58	36	63
Fauchere	36	92	80	56	84	56	31	65
Lawson	33	86	79	55	84	54	27	63
EM	31	92	77	57	85	55	28	64
Wolfenden	28	43	62	62	28	56	97	56
YOU	0	0	0	48	0	0	100	48

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Table 2. Low Resolution Accuracy (Sorting on column 1 - highlighted)

	Per-segment accuracy			Per-residue accuracy
Method ?	Qok ?	Qhtm %obs ?	Qhtm %prd ?	Q2 ?	Q2T %obs ?	Q2T %prd ?	Q2N %obs ?	Q2N %prd ?
TMHMM1	72	91	92	90	83	80	91	92
PHDpsiHtm08	67	95	94	89	87	77	92	96
HMMTOP2	66	94	93	90	85	83	91	91
PRED-TMR	58	92	93	90	78	86	94	89
PHDhtm08	57	86	86	87	83	75	90	94
PHDhtm07	56	85	86	87	83	75	90	94
SOSUI	49	88	86	88	79	72	88	90
TopPred2	48	84	79	88	74	71	93	89
DAS	39	93	81	86	65	85	97	84
Ben-Tal	35	79	90	87	67	83	95	85
Wolfenden	29	56	82	80	47	76	97	79
WW	27	90	75	81	83	59	77	89
GES	23	93	68	78	87	53	72	91
Eisenberg	20	90	63	72	89	47	63	91
KD	13	88	59	63	91	42	50	91
Sweet	11	87	59	58	88	38	44	87
Hopp-Woods	11	87	58	54	90	36	38	88
Heijne	11	89	55	51	91	35	33	89
Av-Cid	10	87	58	53	89	36	38	87
Roseman	9	89	56	48	91	34	30	88
Nakashima	9	88	56	50	90	35	34	87
Levitt	9	88	56	49	91	35	32	88
Lawson	8	86	57	43	89	32	24	83
A-Cid	8	87	57	52	89	35	36	87
Radzicka	6	87	56	41	91	32	21	85
Bull-Breese	6	86	56	40	91	32	20	83
Fauchere	5	87	56	43	91	33	23	86
EM	5	89	56	41	91	32	21	85
YOU	2	0	0	71	0	0	100	71

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Table 3. Confusion with Globular Proteins (Sorting on column 1 - highlighted)

Method	False Positives	High-resolution	Low-resolution
YOU	0	0	0
SOSUI	1	8	4
TMHMM1	1	8	4
PHDhtm08	2	19	23
PHDpsihtm	2	3	8
Wolfenden	2	39	13
Ben-Tal	3	11	4
PHDhtm07	3	14	16
PRED-TMR	4	8	1
HMMTOP2	6	0	1
TopPred2	10	8	11
DAS	16	0	0
WW	32	0	0
GES	53	0	0
Eisenberg	66	0	0
KD	81	0	0
Sweet	84	0	0
Hopp-Woods	89	0	0
Nakashima	90	0	0
Heijne	92	0	0
Levitt	93	0	0
A-Cid	95	0	0
Av-Cid	95	0	0
Roseman	95	0	0
Lawson	98	0	0
FM	99	0	0
Fauchere	99	0	0
Bull-Breese	100	0	0
Radzicka	100	0	0

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Table 4. Confusion with Signal Peptides

Method	% of proteins with signal proteins
YOU	0
PHDpsihtm08	23
PHDhtm08	24
Wolfenden	26
TMHMM1	34
PRED-TMR	41
PHDhtm07	45
HMMTOP2	48
Ben-Tal	57
SOSUI	61
TopPred2	82
WW	90
DAS	97
GES	98
A-Cid	99
Av-Cid	99
Bull-Breese	99
EM	99
Eisenberg	99
Fauchere	99
Heijne	99
Hopp-Woods	99
KD	99
Lawson	99
Levitt	99
Nakashima	99
Radzicka	99
Roseman	99
Sweet	99

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