Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg25099-000007.16.0

>Affy.ctg25099-000007.16.0 MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSXFIPEGL QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN



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.

1.2156941 (Rhod)opsin GPCRDB (Rhod)opsin
  1.2777354 Rhodopsin Vertebrate GPCRDB Rhodopsin Vertebrate
   0.9897409 Rhodopsin Vertebrate type 3 GPCRDB Rhodopsin Vertebrate type 3
  -0.9545728 Rhodopsin Vertebrate type 4
  -0.9754713 Rhodopsin Vertebrate type 2
  -1.0148227 Rhodopsin Vertebrate type 1
  -1.0629444 Rhodopsin Vertebrate type 5
 -1.025352 Rhodopsin Other
 -1.0919536 Rhodopsin Arthropod
 -1.2524402 Rhodopsin Mollusc
-1.0092534Gonadotropin-releasing hormone
-1.0252715Class A Orphan/other
-1.1010183Viral
-1.1093637Thyrotropin-releasing hormone & Secretagogue
-1.1095983Prostanoid
-1.1129171Hormone protein
-1.1388688Melatonin
-1.1438309Olfactory
-1.1941974Peptide
-1.2048038Cannabis
-1.2301649Nucleotide-like
-1.2784905Platelet activating factor
-1.286438Lysosphingolipid & LPA (EDG)
-1.3081601Amine


View all predicted Class A Rhodopsin like peptides

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 17 Class B Secretin like and 11 Class C Metabotropic glutamate / pheromone and 2 Class D Fungal pheromone and 5 Frizzled/Smoothened family and 66 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" http://www.cse.ucsc.edu/research/compbio/gpcr-subclass [postscript, pdf]