Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg13390-000002.23.0

>Affy.ctg13390-000002.23.0 MDSSAAPTNASNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCP PTGSPSMITAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALAT STLPFQSVNYLMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDF RTPRNAKIINVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFI FAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHI YVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNI EQQNSTRIRQNTRDHPSTANTVDRTNHQLENLEAETAPLP



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.

1.2998297 Peptide GPCRDB Peptide
  1.3051996 Opioid GPCRDB Opioid
   1.0595592 Opioid type M GPCRDB Opioid type M
  -0.68318045 Opioid type K
  -0.94906217 Opioid type D
  -0.9750538 Opioid type X
 -0.8582665Somatostatin
 -0.8917308Galanin
 -0.97414064Chemokine/chemotactic factors like
 -1.0043036Neurotensin
 -1.0059862Tachykinin
 -1.0107288Fmet-leu-phe
 -1.0131747CCK
 -1.018115Urotensin II
 -1.0366752Angiotensin
 -1.0491529Proteinase activated
 -1.0596302Endothelin
 -1.0783566Melanocortin
 -1.128503Neuropeptide Y
 -1.1331043Orexin
 -1.1425076APJ like
 -1.1497265Bombesin
 -1.1685464Chemokine
 -1.1908216Bradykinin
 -1.192693Vasopressin-like
 -1.2326205C5a anaphylatoxin
 -1.2451732Interleukin-8
 -1.2520128Thrombin
-0.88979524Thyrotropin-releasing hormone & Secretagogue
-0.8960814Nucleotide-like
-0.9427691Melatonin
-0.98446774Gonadotropin-releasing hormone
-1.0229081Amine
-1.0382142Class A Orphan/other
-1.0794781Viral
-1.0955229Prostanoid
-1.1189282(Rhod)opsin
-1.1231Hormone protein
-1.1670552Cannabis
-1.1863226Platelet activating factor
-1.2464869Lysosphingolipid & LPA (EDG)
-1.2561965Olfactory


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 79 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]