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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
5tat 0 144 124 H H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693960 AAP33763 tat 0 86 79 D D Undecided


Detailed result for 5tat (major) Outlierness: 2.18733 (all), 31.9294 (group)
Subtype Posterior Probability
01_AE 8.81564e-23
A 0.0000000000135957
B 4.7864e-24
C 0.0000000000919152
D 0.000000900741
F 0.0000000000586455
G 9.54344e-24
H 0.999999
J 0.0000000350178
K 0.000000327393

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    53   0   0   0   0   0   0   0   0   0
    A         6  52   1   0   0   1   1   1   0   1
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   2   9   0   1   0   0
    G         0   0   0   0   0   0  15   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 16.7822 (all), 19.5062 (group)
Subtype Posterior Probability
04_cpx 5.84378e-21
H 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 6 at 4 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