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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 0 636 434 B B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60205 CAA40692 env 0 211 150 B B B (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.589899 (all), 0.275672 (group)
Subtype Posterior Probability
01_AE 0
A 1.33862e-33
B 1
C 3.10675e-30
D 1.56757e-20
F 3.90208e-29
G 4.39099e-39
H 3.59299e-24
J 6.18496e-37
K 3.99367e-20

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 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   1   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.159702 (all), 0.172992 (group)
Subtype Posterior Probability
03_AB 0.0000126953
07_BC 0
08_BC 0
12_BF 1.53868e-20
14_BG 0.000412772
15_01B 0.000000164381
B 0.999574

Cross-Validation of Discriminant Models
Miss-Classification Rate: 16 / 484 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0     0      0   0
   07_BC      0    10     0     0     0      0   0
   08_BC      0     1     1     0     0      0   0
   12_BF      0     0     0     8     0      0   2
   14_BG      0     0     0     0     0      0   3
   15_01B     0     0     0     0     0      4   0
   B          1     0     0     0     1      7 445

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