BMC Bioinformatics

Table 1 Sequence-to-topology SVM performance using the LRG and PHAT matrices

From: Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier

	No Positional Weighting		Positional Weighting
Substitution Matrix	LRG^a	PHAT^b	LRG^c	PHAT^d	MLP^e
Accuracy	94.0	93.6	93.9	94.3	90.6
Sensitivity	18.3	9.9	28.4	27.2	35.3
Specificity	99.8	100.0	98.9	99.4	94.8
P_non-IPM	94.1	93.6	94.8	94.7	95.1
P_IPM	87.1	94.4	67.0	76.3	34.2
C_PM	0.38	0.30	0.41	0.44	0.30

^a C = 5.0, 1/2 σ² = 0.03, window size = 21
^b C = 5.0, 1/2 σ² = 0.01, window size = 21
^c C = 25.0, 1/2 σ² = 0.40, window size = 21 residues
^d C = 5.0, 1/2 σ² = 0.10, window size = 21 residues
^e hidden layer size = 16, window size = 15 residues

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ISSN: 1471-2105

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