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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 3 571 513 H 08_BC Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
32185602 AAP72764 pol 0 190 177 C B Undecided


Detailed result for pol (major) Outlierness: 1.15496 (all), 11.4659 (group)
Subtype Posterior Probability
01_AE 2.15201e-27
A 1.03311e-24
B 0.000000702937
C 0.0333919
D 2.064e-25
F 1.4543e-38
G 2.07986e-29
H 0.966607
J 0.00000000091162
K 0.0000000000013109

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 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         3  55   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   1   0  45   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   3   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: 0.686985 (all), 3.4e38 (group)
Subtype Posterior Probability
04_cpx 4.7504e-43
07_BC 0.295982
08_BC 0.703762
10_CD 6.07112e-24
C 0.00025618
H 4.96021e-28

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 382 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 10_CD   C   H
   04_cpx      3     0   0   0
   07_BC       0     0   0   0
   08_BC       0     0   0   0
   10_CD       0     3   0   0
   C           0     0 371   0
   H           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