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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 B Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693952 AAP33759 tat 0 82 71 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 3.24336 (all), 62.7985 (group)
Subtype Posterior Probability
01_AE 0.00000000000000234886
A 0.00000000198166
B 0.0742912
C 0.000000000448526
D 0.0000000116303
F 0.355766
G 0.000000000184471
H 0.569941
J 0.0000013654
K 0.000000000000416637

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    51   0   0   0   0   0   2   0   0   0
    A         5  55   1   0   0   0   0   1   0   1
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 306   0   0   0   1   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   1   9   0   2   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: 4.9119 (all), 7.06289 (group)
Subtype Posterior Probability
03_AB 0.0100457
04_cpx 2.2069e-26
05_DF 1.85985e-17
07_BC 0.000000000920934
08_BC 0.00000000000525478
12_BF 0.000111596
14_BG 0.000107794
15_01B 7.9821e-34
B 0.989735
F 0.000000000332704
H 0.000000249896

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 197 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 05_DF 07_BC 12_BF 14_BG 15_01B   B   F   H
   03_AB       0     0     0     0     0      0   0   0   0
   04_cpx      3     0     0     0     0      0   0   0   0
   05_DF       0     3     0     0     0      0   0   0   0
   07_BC       0     0     0     0     0      0   0   0   0
   08_BC       0     0     0     0     0      0   0   0   0
   12_BF       0     0     0     6     0      0   3   1   0
   14_BG       0     0     0     0     2      0   0   0   0
   15_01B      0     0     0     0     0      2   0   0   0
   B           0     1     2     0     0      0 156   0   0
   F           0     0     0     0     0      0   0  12   0
   H           0     0     0     0     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