Support Vector Machine GPCR Subfamily Classification Results for gi|4502387|ref|NP_001699.1|

>gi|4502387|ref|NP_001699.1| opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan); blue cone pigment [Homo sapiens] MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLN YILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPF GNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLFIFCFI VPLSLICFSYTQLLRALKAVAAQQQESATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGL DLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN


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.

1.0121229 (Rhod)opsin GPCRDB (Rhod)opsin
  1.1730404 Rhodopsin Vertebrate GPCRDB Rhodopsin Vertebrate
   1.0106878 Rhodopsin Vertebrate type 3 GPCRDB Rhodopsin Vertebrate type 3
  -0.9500671 Rhodopsin Vertebrate type 2
  -1.0040047 Rhodopsin Vertebrate type 5
  -1.0406854 Rhodopsin Vertebrate type 1
  -1.0567095 Rhodopsin Vertebrate type 4
 -1.0324453 Rhodopsin Arthropod
 -1.0471251 Rhodopsin Other
 -1.410435 Rhodopsin Mollusc
-1.0088654Amine
-1.0325886Gonadotropin-releasing hormone
-1.0361241Viral
-1.0783317Prostanoid
-1.0841799Olfactory
-1.0926054Hormone protein
-1.0984745Nucleotide-like
-1.1216635Thyrotropin-releasing hormone & Secretagogue
-1.1253073Cannabis
-1.188335Platelet activating factor
-1.1901932Melatonin
-1.2151366Class A Orphan/other
-1.2504272Peptide
-1.3399051Lysosphingolipid & 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 71 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]