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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
nef 11 204 84 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
60123 X63044 ltr 296 628 256 B B B (Unambiguous Nested)
nef 13 628 246 B B B (Unambiguous Nested)


Detailed result for nef (major) Outlierness: 0.62289 (all), 0.578074 (group)
Subtype Posterior Probability
01_AE 2.84615e-19
A 0.0000000660869
B 0.99985
C 0.000000000000267729
D 0.000149512
F 0.000000000791095
G 2.87011e-21
H 0.0000000000041729
J 5.86157e-24
K 4.85354e-19

Cross-Validation of Discriminant Models
Miss-Classification Rate: 55 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    46   0   0   1   0   0   0   0   0
    A         3 100   1   1   2   1   0   0   1
    B         1   4 754   2   4   1   0   0   0
    C         0   1   0 494   0   0   2   0   0
    D         0   0  10   0  70   0   0   0   0
    F         0   2   0   2   0   6   0   3   0
    G         0   0   0   4   0   0  32   0   0
    H         0   2   0   1   0   2   0   2   0
    J         2   0   0   0   0   0   0   0   0
    K         1   0   0   1   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (nested) Outlierness: 0.535891 (all), 0.545252 (group)
Subtype Posterior Probability
03_AB 0.000000000117431
07_BC 0.00000000533902
08_BC 0.00000000000466596
12_BF 0.000000832379
14_BG 7.90073e-23
15_01B 7.05486e-23
B 0.999999

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 795 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     0     0     0     0      0   0
   08_BC      0     0     0     0     0      0   0
   12_BF      2     1     0     3     0      0   2
   14_BG      0     0     0     0    14      0   0
   15_01B     0     0     0     0     0      4   0
   B          0     1     2     0     0      1 762

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