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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 J 03_AB Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693852 AAP33709 tat 0 86 79 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 3.27983 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0000000000000168872
A 0.000000153198
B 0.12714
C 0.00000000816117
D 7.35146e-21
F 0.0410525
G 0.0000000000339701
H 0.0016671
J 0.83014
K 0.0000000000081349

Cross-Validation of Discriminant Models
Miss-Classification Rate: 16 / 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   0 307   0   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   1  10   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: 5.94717 (all), 3.4e38 (group)
Subtype Posterior Probability
03_AB 0.997847
05_DF 4.91814e-38
06_cpx 1.87726e-26
07_BC 0.0000000000769243
08_BC 0.00000000811115
11_cpx 1.24129e-38
12_BF 0.000000000000331073
13_cpx 1.68922e-27
14_BG 0.00121537
15_01B 0
B 0.000937744
F 1.57308e-23
J 3.72589e-21

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 210 at 10 Dimensional MDS
         Predicted
Objective 03_AB 05_DF 06_cpx 07_BC 11_cpx 12_BF 13_cpx 14_BG 15_01B   B   F
   03_AB      0     0      0     0      0     0      0     0      0   0   0
   05_DF      0     3      0     0      0     0      0     0      0   0   0
   06_cpx     0     0      6     0      0     0      0     0      0   0   0
   07_BC      0     0      0     0      0     0      0     0      0   0   0
   08_BC      0     0      0     0      0     0      0     0      0   0   0
   11_cpx     0     0      1     0      8     0      0     0      0   0   0
   12_BF      0     0      0     0      0     6      1     0      0   3   0
   13_cpx     0     0      0     0      0     0      3     0      0   0   0
   14_BG      0     0      0     0      0     0      0     2      0   0   0
   15_01B     0     0      0     0      0     0      0     0      2   0   0
   B          1     0      0     1      0     0      0     0      0 157   0
   F          0     0      0     0      0     0      0     0      0   0  12
   J          0     0      0     0      0     0      0     0      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