Support Vector Machine GPCR Subfamily Classification Results for NP_000721

>NP_000721 MDVVDSLLVNGSNITPPCELGLENETLFCLDQPRPSKEWQPAVQILLYSLIFLLSVLGNTLVITVLIRNK RMRTVTNIFLLSLAVSDLMLCLFCMPFNLIPNLLKDFIFGSAVCKTTTYFMGTSVSVSTFNLVAISLERY GAICKPLQSRVWQTKSHALKVIAATWCLSFTIMTPYPIYSNLVPFTKNNNQTANMCRFLLPNDVMQQSWH TFLLLILFLIPGIVMMVAYGLISLELYQGIKFEASQKKSAKERKPSTTSSGKYEDSDGCYLQKTRPPRKL ELRQLSTGSSSRANRIRSNSSAANLMAKKRVIRMLIVIVVLFFLCWMPIFSANAWRAYDTASAERRLSGT PISFILLLSYTSSCVNPIIYCFMNKRFRLGFMATFPCCPNPGPPGARGEVGEEEEGGTTGASLSRFSYSH MSASVPPQ



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.

1.1463572 Peptide GPCRDB Peptide
  0.9356284 CCK GPCRDB CCK
   0.7481626 CCK type A GPCRDB CCK type A
  -1.0728902 CCK type B
  0.085085735 Chemokine GPCRDB Chemokine
  -0.8065696 C-X-C Chemokine
  -1.0386546 C-C Chemokine
  -1.201216 C-X3-C Chemokine
  -1.244412 XC Chemokine
 -0.87719846Tachykinin
 -0.9713285Neuropeptide Y
 -0.98087484Galanin
 -0.9920273Orexin & neuropeptide FF
 -1.0342716Neuromedin U
 -1.0828083Vasopressin-like
 -1.0891837Endothelin
 -1.1011326Bombesin
 -1.1503611Thrombin
 -1.154449GPR37 / endothelin B-like
 -1.1814947Proteinase activated
 -1.1894057Urotensin II
 -1.1977254Fmet-leu-phe
 -1.2215232Melanocortin
 -1.2368844Interleukin-8
 -1.2462499Chemokine receptor-like
 -1.2582924Neurotensin
 -1.2596446Angiotensin
 -1.2617328Adrenomedullin (G10D)
 -1.2909119C5a anaphylatoxin
 -1.32684APJ like
 -1.3298144Somatostatin
 -1.3621799Opioid
 -1.3727102Bradykinin
-0.84102225Thyrotropin-releasing hormone & Secretagogue
-0.9822694Olfactory
-0.995296Class A Orphan/other
-0.9984795Gonadotropin-releasing hormone
-1.0430304Amine
-1.0879265Hormone protein
-1.1072439Prostanoid
-1.1188579Cannabis
-1.130865Melatonin
-1.2194443Platelet activating factor
-1.229799(Rhod)opsin
-1.3027192Viral
-1.3095492Nucleotide-like
-1.3715986Lysosphingolipid & 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 99 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]