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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
pol 0 96 76 B H Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116272845 DQ876102 pol 0 288 222 J H Undecided


Detailed result for pol (major) Outlierness: 1.51495 (all), 1.93192 (group)
Subtype Posterior Probability
01_AE 0.000602583
A 0.00000414117
B 0.5021
C 1.01411e-17
D 0.00000545937
F 0.000000109709
G 0.000000217215
H 0.497253
J 6.16675e-23
K 0.0000348382

Cross-Validation of Discriminant Models
Miss-Classification Rate: 77 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    50   5   0   1   0   0   0   1   0
    A        13  42   0   1   0   0   2   1   0
    B         0   0 150   1  12   3   0   0   2
    C         0   0   4 364   0   0   0   3   0
    D         4   0   7   0  33   2   0   0   0
    F         1   0   1   1   0   7   0   0   2
    G         3   4   0   0   0   0   8   1   0
    H         1   0   0   0   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 1.77601 (all), 16.6424 (group)
Subtype Posterior Probability
03_AB 0.0000000000157722
04_cpx 0.0000274441
07_BC 0.000000443645
08_BC 1.37619e-23
12_BF 0.000000000156869
14_BG 0.00000000000287738
15_01B 0.00000209865
B 0.000567787
H 0.999402

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 190 at 10 Dimensional MDS
         Predicted
Objective 03_AB 04_cpx 08_BC 12_BF 15_01B   B   H
   03_AB      0      0     0     0      0   0   0
   04_cpx     0      1     0     0      1   1   0
   07_BC      0      0     0     0      0   0   0
   08_BC      0      0     0     0      0   0   0
   12_BF      0      0     0     9      0   0   0
   14_BG      0      0     0     0      0   0   0
   15_01B     2      0     0     1      0   0   0
   B          0      0     1     3      0 164   0
   H          0      0     0     0      0   0   3

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