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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 74 58 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60069 Z11141 gag 0 225 162 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.696086 (all), 0.787566 (group)
Subtype Posterior Probability
01_AE 0.000422164
A 0.00301011
B 0.987799
C 0.00207102
D 0.00288334
F 0.00000878556
G 0.00000982607
H 0.0035485
J 0.0000233133
K 0.000224154

Cross-Validation of Discriminant Models
Miss-Classification Rate: 206 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    37  30   2   1   1   0   1   0   0
    A        12 111   1   6   1   0   1   0   1
    B         3   9 225  11  12   3   0   1   1
    C        10  31  16 486   0   2   8   0   0
    D         3   3  11   3  56   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: 0.914771 (all), 0.904452 (group)
Subtype Posterior Probability
03_AB 0.0000000110709
07_BC 0.00000426011
08_BC 0.0000113346
12_BF 0.0000341605
14_BG 0.0000000086252
15_01B 0.000000124313
B 0.99995

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 290 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     2     0     0     0      1   0
   08_BC      0     1     4     0     0      0   0
   12_BF      0     0     0     8     0      0   2
   14_BG      0     0     0     0     0      0   0
   15_01B     0     0     0     0     0      4   1
   B          1     0     0     1     1      2 260

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