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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 0 887 763 ? K 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134023406 ABO45560 pol 0 295 261 G 04_cpx Undecided


Detailed result for pol (major) Outlierness: 0.901025 (all), 72.31 (group)
Subtype Posterior Probability
01_AE 2.18156e-35
A 4.15436e-30
B 2.49909e-22
C 1.79189e-34
D 9.32507e-22
F 0.00785351
G 0.0000000000116319
H 0.0000000124323
J 0.000000748164
K 0.992146

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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         1  57   0   1   0   0   0   0   0
    B         0   0 167   0   0   1   0   0   0
    C         0   0   0 370   0   0   0   1   0
    D         0   0   0   0  46   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: 15.0945 (all), 11.7254 (group)
Subtype Posterior Probability
04_cpx 0.759787
06_cpx 0.240213
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 10 at 9 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      1      0 2
   06_cpx      2      2 1
   K           1      0 1

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