Support Vector Machine GPCR Subfamily Classification Results for gi|4504531|ref|NP_000515.1|

>gi|4504531|ref|NP_000515.1| 5-hydroxytryptamine (serotonin) receptor 1A [Homo sapiens] MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNV ANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITD PIDYVNKRTPRPRALISLTWLIGFLISIPPILGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLM LVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAV RQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIM GTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCNFCR 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.

1.3991938 Amine GPCRDB Amine
  0.971019 Serotonin GPCRDB Serotonin
   1.0832624 Serotonin Vertebrate type 1 GPCRDB Serotonin Vertebrate type 1
  -0.5876708 Serotonin Other
  -1.0248003 Serotonin Vertebrate type 7
  -1.028681 Serotonin Insect type 2
  -1.0330703 Serotonin Vertebrate type 5
  -1.0735313 Serotonin Vertebrate type 4
  -1.0955237 Serotonin Vertebrate type 2
  -1.1229602 Serotonin Insect type 1
  -1.1768665 Serotonin Vertebrate type 6
 -0.3437732Octopamine
 -0.90383375Acetylcholine (muscarinic)
 -0.9355151Histamine
 -0.95376843Adrenoceptors
 -1.0683339Dopamine
-0.8770784(Rhod)opsin
-0.95171994Hormone protein
-1.0155032Gonadotropin-releasing hormone
-1.0289676Prostanoid
-1.0666244Peptide
-1.1057711Cannabis
-1.1370518Thyrotropin-releasing hormone & Secretagogue
-1.1453191Class A Orphan/other
-1.1980727Melatonin
-1.2021466Olfactory
-1.2386527Platelet activating factor
-1.2451026Viral
-1.3116356Lysosphingolipid & LPA (EDG)
-1.5792595Nucleotide-like




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 19 Class B Secretin like and 11 Class C Metabotropic glutamate / pheromone and 2 Class D Fungal pheromone and 5 Frizzled/Smoothened family and 4 Nematode chemoreceptors and 4 Vomeronasal receptors (V1R & V3R) and 83 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" Bioinformatics 2002 in press [postscript, pdf]