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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 0 127 83 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60067 CAA77481 gag 0 42 30 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.698083 (all), 0.343002 (group)
Subtype Posterior Probability
01_AE 0.0000000000219484
A 0.00000000645184
B 0.999999
C 0.0000000000000298299
D 0.000000427045
F 0.00000000135915
G 0.00000000000000391362
H 0.0000000000472021
J 0.000000635649
K 0.0000000000208114

Cross-Validation of Discriminant Models
Miss-Classification Rate: 31 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    66   5   0   0   1   0   0   0   0   0
    A         2 127   0   0   2   0   1   0   1   0
    B         1   2 258   0   3   0   0   0   1   0
    C         0   0   0 551   0   1   1   0   0   0
    D         0   2   1   1  72   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   0   0   0   0   3   0   0   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.394886 (all), 0.342498 (group)
Subtype Posterior Probability
03_AB 0.00000000000707359
07_BC 0.0000000000000556847
08_BC 1.68775e-19
12_BF 0.000000000654298
14_BG 5.84699e-26
15_01B 1.0285e-16
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 290 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      0     3     0     0      0   0
   08_BC      0     0     5     0      0   0
   12_BF      0     0     0     8      0   2
   14_BG      0     0     0     0      0   0
   15_01B     1     0     0     0      4   0
   B          1     1     0     0      0 263

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