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

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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 34 856 551 B B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
9629357 NC_001802 5tat 5376 5587 185 B B B (Unambiguous Nested)
env 5770 8341 1585 B B B (Unambiguous Nested)
gag 335 1838 963 B B B (Unambiguous Nested)
ltr 8631 9181 256 B B B (Unambiguous Nested)
nef 8342 8963 246 B B B (Unambiguous Nested)
pol 1630 4642 2703 B B B (Unambiguous Nested)
vif 4586 5165 522 B B B (Unambiguous Nested)
vpr 5104 5396 147 B B B (Unambiguous Nested)
vpu 5620 5856 95 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.773941 (all), 0.827586 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.48056e-32
F 9.47567e-37
G 0
H 4.61919e-34
J 3.97969e-43
K 8.68569e-33

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  15   0   0   1
    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 (all), 1 (group)
Subtype Posterior Probability
03_AB 7.02304e-05
07_BC 0
08_BC 0
12_BF 4.90839e-24
14_BG 2.06914e-08
15_01B 2.58236e-06
B 0.999927

Cross-Validation of Discriminant Models
Miss-Classification Rate: 9 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      9     1     0     0      0   0
   08_BC      2     0     0     0      0   0
   12_BF      0     0     8     0      0   2
   14_BG      0     0     0     3      0   0
   15_01B     0     0     0     0      4   0
   B          0     0     0     0      3 451

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