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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
pol 0 297 231 ? D D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
51104139 AAT96767 pol 0 99 79 D D Undecided


Detailed result for pol (major) Outlierness: 3.9983 (all), 10.9933 (group)
Subtype Posterior Probability
01_AE 2.57428e-38
A 2.11963e-31
B 0.00000196278
C 3.25093e-27
D 0.999998
F 2.4494e-25
G 0
H 1.00313e-29
J 0
K 3.29894e-24

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         6  52   0   0   0   0   1   0   0
    B         0   0 160   0   5   3   0   0   0
    C         0   0   0 370   0   0   0   0   1
    D         0   2   0   0  44   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   2   1
    J         0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 12.269 (all), 11.2466 (group)
Subtype Posterior Probability
05_DF 0.00406635
10_CD 1.7373e-18
16_A2D 0
D 0.995934

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 54 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      0     0      0  3
   10_CD      0     1      0  2
   16_A2D     0     0      2  0
   D          2     1      0 43

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