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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 42 30 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60066 Z11130 gag 0 127 83 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.656679 (all), 0.614742 (group)
Subtype Posterior Probability
01_AE 0.0000234034
A 0.0000607139
B 0.998104
C 0.0000638728
D 0.0000688692
F 0.00000175989
G 0.00000325521
H 0.00167242
J 0.000000683912
K 0.000000601816

Cross-Validation of Discriminant Models
Miss-Classification Rate: 222 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    39  25   3   1   4   0   0   0   0   0
    A         9 108   2   5   6   0   2   0   0   1
    B         2   7 218  13  16   1   0   4   1   3
    C        11  26  20 473   8   7   7   0   1   0
    D         1   6   5   2  59   1   1   1   0   0
    F         0   0   1   1   0  11   2   0   0   0
    G         0   1   1   3   4   0  12   0   0   0
    H         0   0   3   0   0   0   0   0   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   1   0   1   0   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.481525 (all), 0.473596 (group)
Subtype Posterior Probability
03_AB 0.000000000100097
07_BC 0.0000000000000274406
08_BC 0.0000000000407887
12_BF 0.000000695845
14_BG 0.00000000128571
15_01B 0.00000000261051
B 0.999999

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      3     0     0     0      0   0
   08_BC      0     5     0     0      0   0
   12_BF      0     0     8     0      0   2
   14_BG      0     0     0     0      0   0
   15_01B     0     0     0     0      4   1
   B          0     2     2     1      3 257

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