Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg15247-000000.4.0

>Affy.ctg15247-000000.4.0 MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC TSSILHLCAIALDRYWAITDPIDYVNKRTPRXXALISLTWLIGFLISIPPMLGWRTPEDR SDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTR HGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNS KEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPF FIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCR Q



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.

1.1341019 Amine GPCRDB Amine
  1.2263789 Serotonin GPCRDB Serotonin
   1.3543338 Serotonin Vertebrate type 1 GPCRDB Serotonin Vertebrate type 1
  -0.9126921 Serotonin Other
  -0.94446844 Serotonin Insect type 2
  -0.9948368 Serotonin Vertebrate type 5
  -0.99815357 Serotonin Vertebrate type 2
  -1.0108595 Serotonin Vertebrate type 7
  -1.0678197 Serotonin Vertebrate type 6
  -1.0812293 Serotonin Insect type 1
  -1.1444303 Serotonin Vertebrate type 4
 -0.92219925Dopamine
 -0.9421737Acetylcholine (muscarinic)
 -0.945332Histamine
 -1.0213362Adrenoceptors
 -1.0383323Octopamine
-1.0217414Gonadotropin-releasing hormone
-1.0756725Class A Orphan/other
-1.079646Prostanoid
-1.1078913Hormone protein
-1.1350821Melatonin
-1.1453675Thyrotropin-releasing hormone & Secretagogue
-1.180046Peptide
-1.1898162Cannabis
-1.221338Viral
-1.2554299Lysosphingolipid & LPA (EDG)
-1.265679Nucleotide-like
-1.275739(Rhod)opsin
-1.3309257Platelet activating factor
-1.3601025Olfactory


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 77 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]