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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 0 169 105 J 11_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134143942 ABO62228 pol 0 56 37 H H Undecided


Detailed result for pol (major) Outlierness: 1.13723 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.00000000216803
A 0.00000197803
B 0.00000131409
C 0.000000000382998
D 0.00000000000130331
F 0.0000000000950765
G 0.000000000000764302
H 0.00000000745732
J 0.999997
K 5.67095e-16

Cross-Validation of Discriminant Models
Miss-Classification Rate: 72 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    53   0   0   4   0   0   0   0   0
    A         7  47   0   1   0   0   4   0   0
    B         0   0 150   0  14   4   0   0   0
    C         5   3   1 359   0   1   1   1   0
    D         0   1   9   0  36   0   0   0   0
    F         0   0   1   2   0   9   0   0   0
    G         0   1   0   8   0   0   7   0   0
    H         0   0   0   2   0   0   0   1   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   1   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: 2.89029 (all), 6.97763 (group)
Subtype Posterior Probability
06_cpx 0.00000000013363
11_cpx 1
13_cpx 0
J 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 19 at 9 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      5      0      0
   11_cpx      0     10      0
   13_cpx      0      0      3
   J           0      0      0

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