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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 61 47 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60071 Z11144 gag 0 183 129 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.8544 (all), 0.995031 (group)
Subtype Posterior Probability
01_AE 0.000308608
A 0.000231714
B 0.999045
C 0.0000893532
D 0.00000900491
F 0.00000000227299
G 0.00000133623
H 0.000173337
J 0.000000316962
K 0.000141394

Cross-Validation of Discriminant Models
Miss-Classification Rate: 207 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    37  29   3   1   1   0   1   0   0   0
    A        13 110   1   6   1   0   1   0   0   1
    B         3  10 223  10  12   3   0   2   1   1
    C        10  30  16 487   1   2   7   0   0   0
    D         3   3  12   3  55   0   0   0   0   0
    F         0   0   1   1   0  11   2   0   0   0
    G         3   1   1   3   1   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   1   2   0   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: 1.02969 (all), 1.04626 (group)
Subtype Posterior Probability
03_AB 0.0000000370853
07_BC 0.0000222918
08_BC 0.000550113
12_BF 0.0000000174344
14_BG 0.00000355801
15_01B 0.000000111728
B 0.999424

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 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     3     0     0     0      0   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