Support Vector Machine GPCR Subfamily Classification Results for NP_056542

>NP_056542 MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYF LVNLAFAEASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAVFASIYSMTAVAFDRYMAIIHPLQP RLSATATKVVICVIWVLALLLAFPQGYYSTTETMPSRVVCMIEWPEHPNKIYEKVYHICVTVLIYFLPLL VIGYAYTVVGITLWASEIPGDSSDRYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLK KFIQQVYLAIMWLAMSSTMYNPIIYCCLNDR



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.

1.0570563 Peptide GPCRDB Peptide
  0.9801231 Tachykinin GPCRDB Tachykinin
   0.09165624 Substance P (NK1) GPCRDB Substance P (NK1)
  -0.8745899 Neuromedin K (NK3)
  -0.9878859 Tachykinin like 2
  -1.0185457 Tachykinin like 1
  -1.1554542 Substance K (NK2)
 -0.983709Galanin
 -1.0566436Neuromedin U
 -1.0901518CCK
 -1.0971296Endothelin
 -1.1275258Thrombin
 -1.1310184Bombesin
 -1.1345968Orexin & neuropeptide FF
 -1.1432264Fmet-leu-phe
 -1.1600143GPR37 / endothelin B-like
 -1.1733838Urotensin II
 -1.1756803Melanocortin
 -1.1767349Neuropeptide Y
 -1.211271Interleukin-8
 -1.2119509Proteinase activated
 -1.2330437Adrenomedullin (G10D)
 -1.2369347Vasopressin-like
 -1.2438471Angiotensin
 -1.256436APJ like
 -1.2749623Neurotensin
 -1.2806576C5a anaphylatoxin
 -1.2993757Chemokine
 -1.3060097Somatostatin
 -1.3145014Chemokine receptor-like
 -1.330068Bradykinin
 -1.3382224Opioid
-0.90580475Thyrotropin-releasing hormone & Secretagogue
-0.9822428Gonadotropin-releasing hormone
-1.0002763Class A Orphan/other
-1.0309489Melatonin
-1.0798403Prostanoid
-1.0961634Cannabis
-1.1053017Hormone protein
-1.1220095Olfactory
-1.1297226(Rhod)opsin
-1.1612802Viral
-1.1715603Platelet activating factor
-1.2436035Nucleotide-like
-1.35009Lysosphingolipid & LPA (EDG)
-1.5523267Amine




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 83 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]