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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 0 75 59 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60111 X60446 gag 0 229 165 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.680049 (all), 0.56031 (group)
Subtype Posterior Probability
01_AE 0.0000476793
A 0.000141137
B 0.987754
C 0.000175553
D 0.0114174
F 0.00000407089
G 0.00000426876
H 0.000411392
J 0.00000820191
K 0.0000362783

Cross-Validation of Discriminant Models
Miss-Classification Rate: 203 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    37  29   3   1   1   0   1   0   0
    A        12 112   1   6   1   0   1   0   0
    B         3   9 225  11  12   3   0   1   1
    C        10  30  16 487   0   2   8   0   0
    D         3   3  10   3  57   0   0   0   0
    F         0   0   1   2   0  10   2   0   0
    G         3   1   1   4   1   0  11   0   0
    H         0   0   3   0   0   0   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   1   2   0   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.492829 (all), 0.560723 (group)
Subtype Posterior Probability
03_AB 0.0000000115912
05_DF 0.000031364
07_BC 0.000000074814
08_BC 0.000000900577
10_CD 0.0000032246
12_BF 0.0000114294
14_BG 0.0000000283694
15_01B 0.000000392129
16_A2D 0.00000222359
B 0.991557
D 0.00839313

Cross-Validation of Discriminant Models
Miss-Classification Rate: 57 / 375 at 10 Dimensional MDS
         Predicted
Objective 03_AB 05_DF 07_BC 08_BC 10_CD 12_BF 14_BG 15_01B 16_A2D   B   D
   03_AB      0     0     0     0     0     0     0      0      0   0   0
   05_DF      0     0     0     0     0     0     0      0      0   0   4
   07_BC      0     0     2     0     0     0     0      1      0   0   0
   08_BC      0     0     1     4     0     0     0      0      0   0   0
   10_CD      0     0     0     0     0     0     0      0      0   0   3
   12_BF      0     0     0     0     0     8     0      0      0   2   0
   14_BG      0     0     0     0     0     0     0      0      0   0   0
   15_01B     0     0     0     0     0     0     0      2      2   0   1
   16_A2D     0     0     0     0     0     0     0      0      0   1   1
   B          1     1     0     0     1     0     1      1      1 247  12
   D          0     4     1     1     1     1     0      0      0  13  55

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