Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg15804-000001.52.0

>Affy.ctg15804-000001.52.0 MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAH KRMRTVTNYFLVNLAFAEASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAVFASI YSMTAVAFDRYMAIIHPLQPRLSATATKVVICVIWVLALLLAFPQGYYSTTETMPSRVVC MIEWPEHPNKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGITLWASEIPGDSSDRYHEQV SAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLAIMWLAMSSTMY NPIIYCCLNDRFRLGFKHAFRCCPFISAGDYEGLEMKSTRYLQTQGSVYKVSRLETTIST VVGAHEEEPEDGPKATPSSLDLTSNCSSRSDSKTMTESFSFSSNVLS



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.

1.2403929 Peptide GPCRDB Peptide
  1.2264936 Tachykinin GPCRDB Tachykinin
   0.9955278 Substance P (NK1) GPCRDB Substance P (NK1)
  -0.71996003 Neuromedin K (NK3)
  -0.851166 Substance K (NK2)
  -1.0678761 Tachykinin like 2
  -1.094017 Tachykinin like 1
 -0.8327225Neuropeptide Y
 -0.9609386Galanin
 -0.9797633Orexin
 -1.009254Neurotensin
 -1.0247257CCK
 -1.0323547Chemokine
 -1.0469729Proteinase activated
 -1.0856357Chemokine/chemotactic factors like
 -1.1101625Melanocortin
 -1.1112547Urotensin II
 -1.116094Bombesin
 -1.1322073Endothelin
 -1.1475664Fmet-leu-phe
 -1.215019Somatostatin
 -1.2306297Vasopressin-like
 -1.239953APJ like
 -1.2517736Angiotensin
 -1.2749481Opioid
 -1.314865Thrombin
 -1.3151664Bradykinin
 -1.338238Interleukin-8
 -1.5155401C5a anaphylatoxin
-0.9645089Melatonin
-0.9722574Thyrotropin-releasing hormone & Secretagogue
-0.98625284Gonadotropin-releasing hormone
-0.99086475(Rhod)opsin
-0.9966497Class A Orphan/other
-1.0633718Nucleotide-like
-1.0758353Viral
-1.1081396Prostanoid
-1.1293077Hormone protein
-1.1670212Cannabis
-1.2151518Olfactory
-1.245088Platelet activating factor
-1.2730165Lysosphingolipid & LPA (EDG)
-1.3873483Amine


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]