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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 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116275837 ABJ93246 pol 0 96 76 H 04_cpx Undecided


Detailed result for pol (major) Outlierness: 2.022 (all), 12.6631 (group)
Subtype Posterior Probability
01_AE 8.48799e-21
A 0.0000000000392278
B 0.0000000000000531595
C 2.27416e-25
D 0.00000000306138
F 0.00722839
G 2.28476e-27
H 0.992765
J 0.0000067468
K 0.0000000000251392

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   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         6  52   0   0   0   0   1   0   0
    B         0   0 159   0   6   3   0   0   0
    C         0   0   0 370   0   0   0   0   1
    D         0   3   0   0  43   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: -19.0194 (all), 29.5197 (group)
Subtype Posterior Probability
04_cpx 1
H 8.34319e-24

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 6 at 5 Dimensional MDS
         Predicted
Objective 04_cpx H
   04_cpx      2 1
   H           2 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