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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
nef 37 111 50 ? B F Undecided
ltr 38 111 59 F F Undecided


Detailed result for nef (major) Outlierness: 4.87919 (all), 5.62331 (group)
Subtype Posterior Probability
01_AE 8.65995e-26
A 0.00000000109144
B 0.874243
C 1.23801e-19
D 0.0000000000000124896
F 0.124225
G 3.06585e-23
H 5.55243e-21
J 0.000000000000191769
K 0.00153145

Cross-Validation of Discriminant Models
Miss-Classification Rate: 118 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    40   0   0   6   0   0   1   0   0   0
    A         0  75  27   5   2   0   0   0   0   0
    B         0   7 737  12  10   0   0   0   0   0
    C         6   1   3 485   0   0   0   1   0   1
    D         0   2   9   0  69   0   0   0   0   0
    F         0   5   4   2   0   1   1   0   0   0
    G         1   0   2   1   0   0  32   0   0   0
    H         0   0   0   6   0   0   0   0   1   0
    J         0   0   0   1   0   1   0   0   0   0
    K         0   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 nef (nested) Outlierness: 5.15022 (all), 7.16062 (group)
Subtype Posterior Probability
03_AB 0.0000146625
05_DF 1.57775e-18
07_BC 0.0000000000000706585
08_BC 0.0000000000000706585
12_BF 0.0000000000000402452
14_BG 2.52234e-44
15_01B 2.15981e-34
B 0.0351989
F 0.964786

Cross-Validation of Discriminant Models
Miss-Classification Rate: 37 / 811 at 10 Dimensional MDS
         Predicted
Objective 05_DF 07_BC 08_BC 12_BF 14_BG 15_01B   B   F
   03_AB      0     0     0     0     0      0   0   0
   05_DF      1     0     0     1     0      0   1   0
   07_BC      0     0     0     0     0      0   0   0
   08_BC      0     0     0     0     0      0   0   0
   12_BF      1     0     0     3     0      0   3   1
   14_BG      1     0     0     0    13      0   0   0
   15_01B     0     0     0     0     0      4   0   0
   B          2     2     1     5     1      0 752   3
   F          0     0     0     2     1      0   9   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 4.90448 (all), 19.9165 (group)
Subtype Posterior Probability
01_AE 1.30415e-30
A 1.73512e-16
B 0.00441234
C 7.80994e-20
D 2.09171e-22
F 0.995588
G 1.75848e-30
H 6.03463e-37
J 1.52057e-21
K 0.000000000138681

Cross-Validation of Discriminant Models
Miss-Classification Rate: 23 / 276 at 10 Dimensional MDS
         Predicted
Objective 01_AE  A  B  C  D  F  G  H  J  K
    01_AE    52  0  0  0  0  0  0  0  0  0
    A         0 19  4  0  0  1  0  0  0  1
    B         0  0 59  0  0  3  0  0  0  0
    C         0  1  0 73  0  0  0  1  0  0
    D         0  0  3  0 35  0  0  0  0  0
    F         0  4  1  0  0  3  0  0  0  0
    G         2  0  0  0  0  0  6  1  0  0
    H         0  1  0  0  0  0  0  2  0  0
    J         0  0  0  0  0  0  0  0  2  0
    K         0  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 ltr (nested) Outlierness: 16.5013 (all), 14.794 (group)
Subtype Posterior Probability
05_DF 0
12_BF 2.75881e-32
F 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 13 at 5 Dimensional MDS
         Predicted
Objective 05_DF 12_BF F
    05_DF     2     0 0
    12_BF     0     2 1
    F         1     0 7

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