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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 0 135 115 H H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693966 AAP33766 tat 0 86 79 D F Undecided


Detailed result for 5tat (major) Outlierness: 1.83104 (all), 11.5112 (group)
Subtype Posterior Probability
01_AE 4.17076e-16
A 0.00000000301833
B 0.000000000000384815
C 0.0000000000303599
D 0.0933875
F 0.0000000355659
G 0.0000000000146013
H 0.90661
J 0.000000000188736
K 0.00000219362

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   K
    01_AE    53   0   0   0   0   0   0   0   0
    A         6  52   1   1   0   0   1   0   2
    B         0   0 159   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0
    F         0   0   0   0   2   9   0   1   0
    G         0   0   0   0   0   0  15   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   1   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: 5.74923 (all), 23.0221 (group)
Subtype Posterior Probability
04_cpx 1.11981e-29
05_DF 0.0000000000000522122
10_CD 1.98731e-38
16_A2D 0.0000000124341
D 0.00115879
H 0.998841

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 57 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 05_DF 10_CD  D  H
   04_cpx      3     0     0  0  0
   05_DF       0     0     0  3  0
   10_CD       0     0     2  0  0
   16_A2D      0     0     0  1  1
   D           0     3     0 41  0
   H           0     0     0  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