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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Nucleotide

Sequence Description: (Link to NCBI GenBank)

Multiple Substitution Correction Algorithm: Jukes-Cantor

All sites that include gaps were deleted.


Gene by Gene Subtype Prediction Summary

Gene Start Stop Length LANL Subtype Major Subtype Nested Analysis Final Decision
env 1 1499 879 D D D D (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60253 CAA79590 env 8 499 308 D D D (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.882614 (all), 0.595144 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 7.91734e-43
C 0
D 1
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   0   0   0   0   0   0   0   0
    A         0  82   0   0   0   0   0   0   0
    B         0   0 454   0   0   0   0   0   0
    C         0   0   0 464   0   0   0   0   0
    D         0   0   0   0  60   0   0   0   0
    F         0   0   0   0   0  16   0   0   0
    G         0   0   0   0   0   0  23   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 1.52846 (all), 1.49631 (group)
Subtype Posterior Probability
05_DF 0
10_CD 7.6521e-19
16_A2D 0
D 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 0 / 68 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      3     0      0  0
   10_CD      0     3      0  0
   16_A2D     0     0      2  0
   D          0     0      0 60

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea