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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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
env 0 291 180 B B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60213 X57450 env 0 875 507 B B B (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.753256 (all), 0.753801 (group)
Subtype Posterior Probability
01_AE 2.62986e-26
A 1.04727e-26
B 1
C 2.51331e-24
D 6.8137e-18
F 0.0000000000000966478
G 2.29705e-32
H 7.03468e-34
J 3.42535e-25
K 3.24222e-16

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   0   0   0   0   0   0   0   0   0
    A         0  81   0   0   0   0   1   0   0   0
    B         0   0 454   0   0   0   0   0   0   0
    C         0   0   0 463   0   1   0   0   0   0
    D         0   0   0   0  60   0   0   0   0   0
    F         0   1   0   0   0  12   0   1   1   1
    G         0   0   0   0   0   0  23   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   0   0   0   0   1   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.501809 (all), 0.62812 (group)
Subtype Posterior Probability
03_AB 0.00149108
07_BC 2.04505e-26
08_BC 3.27052e-26
12_BF 0.0000000305497
14_BG 0.00363634
15_01B 0.000151072
B 0.994721

Cross-Validation of Discriminant Models
Miss-Classification Rate: 14 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF   B
   03_AB      0     0     0   0
   07_BC      8     2     0   0
   08_BC      2     0     0   0
   12_BF      0     0     8   2
   14_BG      0     0     0   3
   15_01B     0     0     0   4
   B          0     0     0 454

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