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Table 2 Coverage (percentage of True Positives identified before the first False Positive) and the average percentage of errors per sequence at the MEP of HMM-d and HMM-ModE for classification of Level-2 sub-families of Class A and Class C GPCR proteins

From: HMM-ModE – Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences

 

Coverage

Average errors per sequence at MEP

 

HMM-ModE

HMM-d

HMM-ModE

HMM-d

 

Set0

Set1

Set0

Set1

Set0

Set1

Set0

Set1

Acetylcholine_muscarinic

1

1

1

0.92

0

0

0

0.08

Adenosine

1

1

1

1

0

0

0

0

Adrenoceptors

0.48

0.97

0.45

0.97

0.06

0.03

0.06

0.03

Adrenomedullin_G10D

1

1

1

1

0

0

0

0

Angiotensin

1

1

1

1

0

0

0

0

APJlike

1

1

1

1

0

0

0

0

Bombesin

1

1

1

1

0

0

0

0

Bradykinin

1

1

1

1

0

0

0

0

C5aanaphylatoxin

1

1

1

1

0

0

0

0

CCK

1

0.89

1

0.89

0

0.11

0

0.11

Chemokinereceptor_like

0.5

0.8

0.5

0.8

0.5

0.2

0.5

0.2

Chemokine

1

0.55

0.98

0.55

0

0.09

0.02

0.11

Dopamine

0.87

0.91

0.87

0.91

0.13

0.09

0.13

0.09

Endothelin

1

1

1

0.88

0.29

0

0.29

0.13

Fmet_leu_phe

1

1

1

1

0

0

0

0

Folliclestimulatinghormone

0.86

1

0.86

1

0.14

0

0.14

0

GABA_Bsubtype1

1

1

1

1

0

0

0

0

GABA_Bsubtype2

1

1

1

1

0

0

0

0

Galaninlike

1

1

1

1

0

0

0

0

GP40like

1

1

1

0.5

0

0

0

0.5

GPR

0.76

0.73

0.76

0.73

0.24

0.27

0.24

0.27

Growthhormonesecretagoguelike

1

1

1

1

0

0

0

0

Growthhormonesecretagogue

1

1

1

1

0

0

0

0

Histamine

1

1

1

1

0

0

0

0

Interleukin_8

1

1

1

1

0

0

0

0

LeukotrieneB4receptorBLT1

1

1

1

1

0

0

0

0

Lutropin_choriogonadotropichormone

1

1

1

1

0

0

0

0

Melanocortin

1

1

1

1

0

0

0

0

MetabotropicglutamategroupIII

1

1

1

1

0

0

0

0

MetabotropicglutamategroupII

1

1

1

1

0

0

0

0

MetabotropicglutamategroupI

1

1

1

1

0

0

0

0

Metabotropicglutamateother

1

1

1

1

1

1

1

1

NeuropeptideY

0.88

1

0.88

1

0.13

0

0.13

0

Neurotensin

1

1

1

1

0

0

0

0

Octopamine

0.29

1

0.29

1

0.71

0

0.71

0

OlfactoryIIfam10

1

1

1

1

0

0

0

0

OlfactoryIIfam1

0.86

0.80

0.86

0.80

0.14

0.10

0.14

0.10

OlfactoryIIfam2

1

1

0.88

1

0

0

0.13

0

OlfactoryIIfam3

1

1

1

1

0

0

0

0

OlfactoryIIfam5

1

0.71

1

0.71

0

0.29

0

0.29

OlfactoryIIfam6

0.83

1

1

1

0.17

0

0

0

OlfactoryIIfam7

1

1

1

0.86

0

0

0

0.14

OlfactoryIIfam8

1

1

1

1

0

0

0

0

Opioid

1

1

1

1

0

0

0

0

Orexin_neuropeptideFF

1

1

1

1

0

0

0

0

PlateletADP_KI01receptors

1

1

1

1

0

0

0

0

Prostacyclin

1

1

1

1

0

0

0

0

Prostaglandin

1

1

1

1

0

0

0

0

Proteinase_activatedlike

1

1

1

1

0

0

0

0

Purinoceptors

1

1

0.91

1

0

0

0.09

0

RDC1

1

1

1

1

0

0

0

0

RhodopsinArthropod

1

1

1

1

0

0

0

0

RhodopsinMollusc

0.6

1

0.6

1

0.4

0

0.4

0

RhodopsinOther

0.86

0.67

0.71

0.50

0.14

0.33

0.29

0.50

RhodopsinVertebrate

1

1

1

1

0

0

0

0

Serotonin

0.94

0.94

0.94

0.94

0.06

0.06

0.06

0.06

Somatostatin

1

1

1

1

0

0

0

0

Tachykinin

0.92

1

0.92

1

0.08

0

0.08

0

Thromboxane

1

1

1

1

0

0

0

0

Thyrotropin_releasinghormone

1

1

1

1

0

0

0

0

Thyrotropin

1

1

1

1

0

0

0

0

UrotensinII

1

1

1

1

0

0

0

0

Vasopressin_like

1

1

1

1

0

0

0

0

Masproto_oncogene

1

1

1

1

0

0

0

0

GPR37_endothelinB_like

1

1

1

1

0

1

0

1

Average

0.95

0.97

0.94

0.95

0.06

0.05

0.07

0.07

Average(set0,set1)

0.96

0.95

0.06

0.07