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

Virus: HIV-1 / Sequence Type: Nucleotide

Sequence Description: (Link to NCBI GenBank)

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 0 230 166 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60104 CAA77494 gag 0 76 60 B B B (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 0.719886 (all), 1.02429 (group)
Subtype Posterior Probability
01_AE 2.61741e-18
A 0.000000000000116473
B 1
C 0.00000000000129444
D 0.00000000000486382
F 2.01405e-16
G 2.35643e-20
H 5.24614e-17
J 0.000000105424
K 0.00000000000000348596

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   2   0   0   0   0   0   0   0   0
    A         1 128   0   0   2   0   1   0   0   1
    B         0   1 262   0   1   1   0   0   0   0
    C         0   0   0 553   0   0   0   0   0   0
    D         0   2   1   0  72   0   1   0   0   0
    F         0   0   0   0   1  14   0   0   0   0
    G         0   0   0   0   0   0  21   0   0   0
    H         0   0   0   0   0   2   0   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 1.36692 (all), 1.4137 (group)
Subtype Posterior Probability
03_AB 0.000000000000536714
07_BC 0.00000000000272294
08_BC 1.69494e-16
12_BF 0.00000000000000409894
14_BG 4.87336e-18
15_01B 1.21135e-23
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     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     0      0 265

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