βhairPred - βhairpin prediction server from protein sequences

SUPPLIMENTARY MATERIAL

There are following six suplimentary materials

Fig:S1

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Diagramatic repesentation of BhairPred Training Algorithm (Fig:S2-S7)

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Performance of BhairPred on Thronton's dataset (Table:S1,S2)

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Number of hairpins found by PROMOTIF in each target protein

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Number of ECE patterns found by PSIPRED and their BhairPred prediction status

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Performance Measurement

Sensitivity Specificity Accuracy MCC Probability of positive prediction Probability of negative prediction

Table S1:Performance of SVM based BhairPred algorithm trained on Thronton's dataset

APPROACH PERCENT COVERAGE PERCENT PROBABILITY ACCURACY MCC

Qo(H) Qo(Nh) Qp(H) Qp(nh)

AA 68.1 63.2 69.4 62.0 65.9 0.31

MSA (1) 77.3 65.7 73.4 70.7 72.1 0.44

AA+ACC_O (2) 78.4 57.06 69 68.12 68.6 0.36

AA+SS_O (3) 65.6 75.1 76.3 64.3 69.9 0.41

HYBRID (1+2+3) 78.8 70.6 76.6 73.3 75.1 0.49

AA+ACC_P (4) 70.8 59.4 68.0 62.8 65.7 0.30

AA+SS_P (5) 60.76 74.8 74.7 61.0 67.1 0.36

HYBRID (1+4+5) 81.5 58.3 70.5 72.4 71.1 0.41

APPROACH	PERCENT COVERAGE	PERCENT PROBABILITY	ACCURACY	MCC
Qo(H)	Qo(Nh)	Qp(H)	Qp(nh)
AA	68.1	63.2	69.4	62.0	65.9	0.31
MSA (1)	77.3	65.7	73.4	70.7	72.1	0.44
AA+ACC_O (2)	78.4	57.06	69	68.12	68.6	0.36
AA+SS_O (3)	65.6	75.1	76.3	64.3	69.9	0.41
HYBRID (1+2+3)	78.8	70.6	76.6	73.3	75.1	0.49
AA+ACC_P (4)	70.8	59.4	68.0	62.8	65.7	0.30
AA+SS_P (5)	60.76	74.8	74.7	61.0	67.1	0.36
HYBRID (1+4+5)	81.5	58.3	70.5	72.4	71.1	0.41

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Table S2:Performance of ANN based BhairPred algorithm trained on Thronton's dataset

APPROACH Qo(H) Qo(Nh) ACCURACY Qp(H) Qp(nh) Sh Snh MCC

AA 45.7 71.9 58.1 69.1 51.2 5.9 16.2 0.19

MSA 45.8 75.9 59.3 70.0 53.3 6.9 20 0.23

AA+SS_O 67.7 75.8 71.3 77.4 65.9 14.7 9.9 0.43

AA+SS_P 55.6 75.8 62.7 70.4 56.8 8.8 11 0.27

AA+ACC_O 55.8 73.5 63.5 72.2 57.7 9.5 13.1 0.28

AA+ACC_P 46.6 68.5 57.1 65.1 51.2 4.8 13.1 0.16

Seq-Str Newtowrk (SS_P) 55.1 74.8 63.9 73.3 57.8 9.7 14.7 0.31
Seq-Str Newtowrk (SS_O) 64.9 74.3 69.1 75.7 63.4 13.1 9.5 0.39

APPROACH	Qo(H)	Qo(Nh)	ACCURACY	Qp(H)	Qp(nh)	Sh	Snh	MCC
AA	45.7	71.9	58.1	69.1	51.2	5.9	16.2	0.19
MSA	45.8	75.9	59.3	70.0	53.3	6.9	20	0.23
AA+SS_O	67.7	75.8	71.3	77.4	65.9	14.7	9.9	0.43
AA+SS_P	55.6	75.8	62.7	70.4	56.8	8.8	11	0.27
AA+ACC_O	55.8	73.5	63.5	72.2	57.7	9.5	13.1	0.28
AA+ACC_P	46.6	68.5	57.1	65.1	51.2	4.8	13.1	0.16
Seq-Str Newtowrk (SS_P)	55.1	74.8	63.9	73.3	57.8	9.7	14.7	0.31
Seq-Str Newtowrk (SS_O)	64.9	74.3	69.1	75.7	63.4	13.1	9.5	0.39

AA:Amino Acid Sequence: MSA:Multiple Sequence Alignment; ACC_O:Observed Accessibility; ACC_P:Predicted Accessibility; SS_O:Observed Secondary Structure; SS_P:Predicted Secondary Structure

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Figure S2:Training scheme of ANN