Support Vector Machine GPCR Subfamily Classification Results for NP_001828

>NP_001828 MTTSLDTVETFGTTSYYDDVGLLCEKADTRALMAQFVPPLYSLVFTVGLLGNVVVVMILIKYRRLRIMTN IYLLNLAISDLLFLVTLPFWIHYVRGHNWVFGHGMCKLLSGFYHTGLYSEIFFIILLTIDRYLAIVHAVF ALRARTVTFGVITSIVTWGLAVLAALPEFIFYETEELFEETLCSALYPEDTVYSWRHFHTLRMTIFCLVL PLLVMAICYTGIIKTLLRCPSKKKYKAIRLIFVIMAVFFIFWTPYNVAILLSSYQSILFGNDCERSKHLD LVMLVTEVIAYSHCCMNPVIYAFVGERFRKYLRHFFHRHLLMHLGRYIPFLPSEKLERTSSVSPSTAEPE LSIVF



Here is a list of Class A Rhodopsin like subfamilies with support vector machine models and the score this sequence received with respect to each model.

1.3039129 Peptide GPCRDB Peptide
  0.9938634 Chemokine GPCRDB Chemokine
   0.9622094 C-C Chemokine GPCRDB C-C Chemokine
    1.0744588 C-C Chemokine type 3 GPCRDB C-C Chemokine type 3
   -0.66729736 C-C Chemokine type 1
   -0.9523224 C-C Chemokine type 8
   -0.95840263 C-C Chemokine other
   -0.98825854 C-C Chemokine type 10
   -0.9889066 C-C Chemokine type 5
   -1.0254989 C-C Chemokine type 11
   -1.0473578 C-C Chemokine type 4
   -1.0537488 C-C Chemokine type X
   -1.0793059 C-C Chemokine type 6
   -1.1152236 C-C Chemokine type 7
   -1.1226537 C-C Chemokine type 2
   -1.137615 C-C Chemokine type 9
  -0.9013303 C-X-C Chemokine
  -0.9326917 C-X3-C Chemokine
  -1.0068629 XC Chemokine
 -0.8771268Angiotensin
 -0.95312643Tachykinin
 -0.97231466Galanin
 -0.99976635Interleukin-8
 -1.021345Thrombin
 -1.0469798Fmet-leu-phe
 -1.0960078Endothelin
 -1.097416Neuromedin U
 -1.1212747Bradykinin
 -1.121978CCK
 -1.1275139Urotensin II
 -1.1307805C5a anaphylatoxin
 -1.1461692Adrenomedullin (G10D)
 -1.1542635Chemokine receptor-like
 -1.1601915APJ like
 -1.167386Bombesin
 -1.1750944Melanocortin
 -1.1787305GPR37 / endothelin B-like
 -1.2707486Opioid
 -1.2770808Proteinase activated
 -1.3054206Vasopressin-like
 -1.3058795Neurotensin
 -1.3182139Orexin & neuropeptide FF
 -1.3468902Somatostatin
 -1.6166239Neuropeptide Y
-0.6658858Nucleotide-like
-0.8806458Viral
-0.98151386Hormone protein
-0.98220545Amine
-0.9867845Gonadotropin-releasing hormone
-1.0221636Thyrotropin-releasing hormone & Secretagogue
-1.0339667Class A Orphan/other
-1.0483662(Rhod)opsin
-1.063175Olfactory
-1.067434Platelet activating factor
-1.0876222Prostanoid
-1.0985436Melatonin
-1.1286564Cannabis
-1.3484125Lysosphingolipid & LPA (EDG)




HOW TO INTERPRET THE SCORES:

Subfamily Scoring:

The support vector machine for each subfamily is trained to score positive examples (members of the subfamily) as 1.0 and negative examples (non-members) as -1.0

If this sequence receives a negative score with respect to a subfamily, it is probably not a member of the subfamily.

If this sequence receives a positive score with respect to a subfamily, it is probably in the subfamily.

In general, the score's distance from zero gives you the confidence level of the prediction. Positive scores greater than +1.0 mean a classifier has strongly accepted your sequence. Negative scores less than -1.0 mean a classifier has strongly rejected your sequence. For a more detailed evaluation of scores and confidence levels, take a look at Classification Statistics.
SOME ADDITIONAL INFORMATION:

There were 19 Class B Secretin like and 11 Class C Metabotropic glutamate / pheromone and 2 Class D Fungal pheromone and 5 Frizzled/Smoothened family and 4 Nematode chemoreceptors and 4 Vomeronasal receptors (V1R & V3R) and 88 Class A Rhodopsin like subfamilies whose classifiers were not run, because the families or subfamilies that contain them were rejected by classifiers higher in the hierarchy. For example, if the Amine receptor classifier scores this sequence negatively, it will not be checked with respect to the subfamilies of Amine receptors (Histamine, Serotonin, Dopamine, Octopamine and Acetylcholine (muscarinic) receptors).

Not all subfamilies have models yet. This sequence may be in a subfamily that has not yet been modeled.

Please cite: R. Karchin, K. Karplus and D. Haussler "Classifying G-Protein Coupled Receptors with Support Vector Machines" Bioinformatics 2002 in press [postscript, pdf]