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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
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