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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
gag 35 500 337 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 gag (major) Outlierness: 0.553132 (all), 0.8122 (group)
Subtype Posterior Probability
01_AE 1.94224e-22
A 2.52038e-31
B 1
C 1.3777e-24
D 7.65713e-11
F 5.50019e-22
G 8.09168e-29
H 4.49254e-28
J 2.57987e-16
K 1.27168e-14

Cross-Validation of Discriminant Models
Miss-Classification Rate: 16 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    72   0   0   0   0   0   0   0   0   0
    A         0 126   0   1   0   0   2   3   1   0
    B         0   0 261   0   2   0   0   0   0   2
    C         0   0   0 552   0   0   1   0   0   0
    D         0   0   0   0  76   0   0   0   0   0
    F         0   0   0   0   0  14   0   0   0   1
    G         0   0   0   0   0   0  21   0   0   0
    H         0   1   0   0   0   0   0   2   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   1   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.328093 (all), 0.559286 (group)
Subtype Posterior Probability
03_AB 3.80006e-22
07_BC 2.29257e-39
08_BC 8.0573e-32
12_BF 8.10858e-15
14_BG 1.64871e-26
15_01B 1.80319e-39
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      3     0     0      0   0
   08_BC      0     5     0      0   0
   12_BF      0     0     9      0   1
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     1      0 264

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