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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 38 245 181 ? B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60145 CAA45921 tat 0 86 79 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 0.678238 (all), 0.402616 (group)
Subtype Posterior Probability
01_AE 5.63031e-32
A 1.37078e-23
B 1
C 8.73364e-34
D 0.000000000228203
F 9.00826e-24
G 1.84257e-25
H 7.47376e-34
J 4.07687e-20
K 3.55778e-24

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    52   1   0   0   0   0   0   0   0   0
    A         2  58   1   0   0   0   2   0   0   0
    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   0   0  44   0   0   0   0   0
    F         0   0   0   0   0  11   0   0   0   1
    G         1   0   0   0   0   0  14   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: 0.68516 (all), 0.740981 (group)
Subtype Posterior Probability
03_AB 0.00112693
07_BC 1.471e-18
08_BC 6.08088e-31
12_BF 0.000000509419
14_BG 1.07381e-20
15_01B 7.9449e-29
B 0.998873

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 176 at 10 Dimensional MDS
         Predicted
Objective 03_AB 12_BF 14_BG 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      0     0     0      0   0
   08_BC      0     0     0      0   0
   12_BF      0     7     0      0   3
   14_BG      0     0     2      0   0
   15_01B     0     0     0      2   0
   B          1     0     0      0 158

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