Support Vector Machine GPCR Subfamily Classification Results for Affy.ctg10-000000.8.0

>Affy.ctg10-000000.8.0 MDVVDSLLVNGSNITPPCELGLENETLFCLDQPRPSKEWQPAVQILLYSLIFLLSVLGNT LVITVLIRNKRMRTVTNIFLLSLAVSDLMLCLFCMPFNLIPNLLKDFIFGSAVCKTTTYF MGTSVSVSTFNLVAISLERYGAICKPLQSRVWQTKSHALKVIAATWCLSFTIMTPYPIYS NLVPFTKNNNQTANMCRFLLPNDVMQQSWHTFLLLILFLIPGIVMMVAYGLISLELYQGI KFEASQKKSAKERKPSTTSSGKYEDSDGCYLQKTRPPRKLELRQLSTGSSSRANRIRSNS SAANLMAKKRVIRMLIVIVVLFFLCWMPIFSANAWRAYDTASAERRLSGTPISFILLLSY TSSCVNPIIYCFMNKRFRLGFMATFPCCPNPGPPGARGEVGEEEEGGTTGASLSRFSYSH MSASVPPQ



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.

1.2488102 Peptide GPCRDB Peptide
  0.9388786 CCK GPCRDB CCK
   0.99513286 CCK type A GPCRDB CCK type A
  -0.722624 CCK type B
 -0.93278694Tachykinin
 -0.97620475Orexin
 -0.97860503Galanin
 -0.98566073Vasopressin-like
 -0.9926803Neuropeptide Y
 -1.0125729Neurotensin
 -1.0397019Proteinase activated
 -1.0812371Chemokine/chemotactic factors like
 -1.1220864Bombesin
 -1.1322601Urotensin II
 -1.1393555Chemokine
 -1.1428814Endothelin
 -1.1875098Melanocortin
 -1.2092745Fmet-leu-phe
 -1.2375767Somatostatin
 -1.3063738Angiotensin
 -1.3075612Opioid
 -1.3322483APJ like
 -1.3408463Thrombin
 -1.3737104Interleukin-8
 -1.3784285Bradykinin
 -1.5376443C5a anaphylatoxin
-0.85081005Thyrotropin-releasing hormone & Secretagogue
-1.0119679Gonadotropin-releasing hormone
-1.0348245Class A Orphan/other
-1.0642909Melatonin
-1.0831629Olfactory
-1.1160269Hormone protein
-1.15334Prostanoid
-1.1810931Nucleotide-like
-1.1863198(Rhod)opsin
-1.2024751Cannabis
-1.260504Viral
-1.307442Platelet activating factor
-1.3141844Amine
-1.3183128Lysosphingolipid & LPA (EDG)


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 81 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]