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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 0 288 222 F 12_BF Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116275959 ABJ93307 pol 0 96 76 F 12_BF Undecided


Detailed result for pol (major) Outlierness: 1.72357 (all), 14.405 (group)
Subtype Posterior Probability
01_AE 5.06667e-21
A 0.0000000000000208483
B 0.0000518131
C 1.09047e-26
D 8.91689e-16
F 0.999948
G 4.57984e-19
H 0.0000000000060374
J 0.000000000000151516
K 0.000000000371338

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 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  53   0   0   0   0   0   0   0
    B         0   0 159   0   6   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   1  11   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: 5.57709 (all), 9.26137 (group)
Subtype Posterior Probability
05_DF 4.44212e-43
12_BF 0.999994
F 0.00000640221

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 24 at 10 Dimensional MDS
         Predicted
Objective 05_DF 12_BF F
    05_DF     3     0 0
    12_BF     0     7 2
    F         0     5 7

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