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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
gag 1 181 128 K 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
1556508 AAB08994 gag 0 60 47 K K Undecided


Detailed result for gag (major) Outlierness: 2.29992 (all), 16.0206 (group)
Subtype Posterior Probability
01_AE 9.41361e-20
A 9.9788e-20
B 6.31142e-17
C 0.0000000000340156
D 0.00000000000725909
F 0.00000000547009
G 0.000000010988
H 0.000417176
J 1.21649e-22
K 0.999583

Cross-Validation of Discriminant Models
Miss-Classification Rate: 33 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    67   3   0   1   1   0   0   0   0   0
    A         2 128   0   0   2   0   1   0   0   0
    B         0   1 260   0   3   0   0   0   1   0
    C         0   0   0 549   0   1   3   0   0   0
    D         0   2   2   0  71   1   0   0   0   0
    F         0   0   0   0   0  15   0   0   0   0
    G         0   1   0   0   0   0  19   1   0   0
    H         0   0   0   0   0   1   1   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   3   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 2.74228 (all), 5.68887 (group)
Subtype Posterior Probability
04_cpx 1.82169e-43
06_cpx 1
K 1.48524e-24

Cross-Validation of Discriminant Models
Miss-Classification Rate: 0 / 15 at 8 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      3      0 0
   06_cpx      0      9 0
   K           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