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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 H H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116275305 ABJ92981 pol 0 96 76 D K Undecided


Detailed result for pol (major) Outlierness: 1.73678 (all), 17.6801 (group)
Subtype Posterior Probability
01_AE 1.4601e-22
A 0.000000000000138633
B 0.0000000000263153
C 7.08652e-18
D 0.00000000204249
F 0.0000166549
G 3.51212e-26
H 0.99871
J 0.0012736
K 0.00000000000117615

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    57   0   0   0   0   0   0   0   0   0
    A         5  53   0   0   0   0   1   0   0   0
    B         0   0 159   0   6   3   0   0   0   0
    C         0   0   0 370   0   0   0   0   0   1
    D         0   3   0   0  43   0   0   0   0   0
    F         0   0   0   0   1  11   0   0   0   0
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   0   0   0   2   1   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   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: 13.0053 (all), 15.7542 (group)
Subtype Posterior Probability
04_cpx 0.101827
H 0.898173

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 6 at 6 Dimensional MDS
         Predicted
Objective 04_cpx H
   04_cpx      1 2
   H           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