Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg16551-000000.2.0

>Affy.ctg16551-000000.2.0 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA



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.

1.3737946 (Rhod)opsin GPCRDB (Rhod)opsin
  1.2046182 Rhodopsin Vertebrate GPCRDB Rhodopsin Vertebrate
   1.1593665 Rhodopsin Vertebrate type 1 GPCRDB Rhodopsin Vertebrate type 1
  -0.951006 Rhodopsin Vertebrate type 4
  -1.0109006 Rhodopsin Vertebrate type 3
  -1.0270004 Rhodopsin Vertebrate type 2
  -1.0422791 Rhodopsin Vertebrate type 5
 -1.007305 Rhodopsin Arthropod
 -1.0099819 Rhodopsin Other
 -1.2324762 Rhodopsin Mollusc
-1.0134108Gonadotropin-releasing hormone
-1.0463047Melatonin
-1.0558361Thyrotropin-releasing hormone & Secretagogue
-1.0751076Prostanoid
-1.085703Viral
-1.0876032Peptide
-1.0894443Class A Orphan/other
-1.1367735Hormone protein
-1.1580536Cannabis
-1.2250566Lysosphingolipid & LPA (EDG)
-1.2650588Platelet activating factor
-1.2732904Nucleotide-like
-1.3201474Olfactory
-1.479893Amine


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]