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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
pol 0 99 79 ? D D D (Major agrees Nested with high confidence)


Detailed result for pol (major) Outlierness: 0.646947 (all), 0.918695 (group)
Subtype Posterior Probability
01_AE 0.00000398875
A 0.000000126967
B 0.275226
C 0.00000029709
D 0.724731
F 0.0000380999
G 0.00000000259696
H 2.54145e-16
J 1.55269e-22
K 0.000000000587359

Cross-Validation of Discriminant Models
Miss-Classification Rate: 82 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    50   5   0   1   0   0   0   1   0
    A        14  39   0   1   0   0   4   1   0
    B         0   0 149   1  13   3   0   0   2
    C         1   0   4 363   0   0   0   3   0
    D         4   0   7   0  33   2   0   0   0
    F         1   0   1   1   0   7   0   0   2
    G         3   4   0   0   0   0   8   1   0
    H         1   0   0   0   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.385231 (all), 0.364401 (group)
Subtype Posterior Probability
03_AB 0.00000000183598
05_DF 0.00363539
07_BC 0.0022825
08_BC 0.00000000852846
10_CD 0.000203483
12_BF 0.000000103913
14_BG 0.00000000000616589
15_01B 0.00000000703315
16_A2D 7.06259e-18
B 0.34249
D 0.651389

Cross-Validation of Discriminant Models
Miss-Classification Rate: 43 / 238 at 10 Dimensional MDS
         Predicted
Objective 03_AB 05_DF 07_BC 08_BC 10_CD 12_BF 14_BG 16_A2D   B   D
   03_AB      0     0     0     0     0     0     0      0   0   0
   05_DF      0     0     0     0     0     0     0      0   2   1
   07_BC      0     0     0     0     0     0     0      0   0   0
   08_BC      0     0     0     0     0     0     0      0   0   0
   10_CD      0     0     0     0     0     0     0      0   0   3
   12_BF      0     0     0     0     0     9     0      0   0   0
   14_BG      0     0     0     0     0     0     0      0   0   0
   15_01B     1     0     0     0     0     1     1      0   0   0
   16_A2D     0     0     0     0     0     0     1      1   0   0
   B          0     0     0     1     0     5     0      0 151  11
   D          0     1     1     0     2     0     0      0   8  34

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