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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 66 52 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60110 X60445 gag 0 199 145 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.553859 (all), 0.524719 (group)
Subtype Posterior Probability
01_AE 0.000883324
A 0.00155879
B 0.992393
C 0.00317211
D 0.00178127
F 0.00000108996
G 0.0000122061
H 0.0000296599
J 0.0000538181
K 0.000114369

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  29   3   1   1   0   1   0   0
    A        12 111   1   6   1   0   1   0   1
    B         3  10 225  10  12   3   0   1   1
    C        10  31  16 486   0   2   8   0   0
    D         3   3  12   3  55   0   0   0   0
    F         0   0   1   1   0  11   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: 0.328448 (all), 0.348509 (group)
Subtype Posterior Probability
03_AB 0.000000468281
07_BC 0.00000100619
08_BC 0.000000955087
12_BF 0.00000905314
14_BG 0.00000000200131
15_01B 0.00000150334
B 0.999987

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 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     2     1      2 259

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