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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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 96 76 J J Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116272721 DQ876040 pol 0 288 222 J F Undecided


Detailed result for pol (major) Outlierness: 2.42008 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0000000000905171
A 0.00189833
B 0.00000000000151939
C 7.97883e-25
D 1.33963e-18
F 0.000000131494
G 0.00198902
H 0.0000000115843
J 0.996113
K 0.0000000000000053504

Cross-Validation of Discriminant Models
Miss-Classification Rate: 80 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    49   6   0   1   0   0   0   1   0
    A        12  43   0   1   0   0   3   0   0
    B         0   0 149   1  13   3   0   0   2
    C         1   0   4 363   0   0   0   3   0
    D         4   0   8   0  32   2   0   0   0
    F         2   0   0   1   0   7   0   0   2
    G         3   4   0   0   0   0   8   1   0
    H         1   0   0   0   0   0   0   2   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: 4.37058 (all), 3.4e38 (group)
Subtype Posterior Probability
06_cpx 0.0000000000426595
11_cpx 1.7805e-17
13_cpx 6.99776e-28
J 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 19 at 9 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      5      0      0
   11_cpx      1      9      0
   13_cpx      0      0      3
   J           0      0      0

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