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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
env 0 209 112 B B B B (Unambiguous Nested)
nef 210 794 221 B B B (Unambiguous Nested)
ltr 462 985 256 B B B (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.783135 (all), 0.632724 (group)
Subtype Posterior Probability
01_AE 3.11967e-33
A 2.15702e-20
B 0.999996
C 7.95689e-28
D 0.00000447288
F 0.00000000000753293
G 0.0000000000000125366
H 0.000000000167148
J 1.48655e-19
K 0.0000000000000365175

Cross-Validation of Discriminant Models
Miss-Classification Rate: 24 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   0   0   0   0   0   0   0   0
    A         4  72   0   0   3   0   2   1   0
    B         0   0 450   0   2   0   0   2   0
    C         0   0   0 464   0   0   0   0   0
    D         0   0   2   0  55   1   1   1   0
    F         0   0   0   0   2  14   0   0   0
    G         0   0   0   0   0   0  23   0   0
    H         0   0   0   0   1   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.596944 (all), 0.553374 (group)
Subtype Posterior Probability
03_AB 0.00000000000000151766
07_BC 1.70593e-33
08_BC 2.8026e-45
12_BF 0.000253855
14_BG 1.05474e-38
15_01B 1.06872e-36
B 0.999746

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC     10     0     0     0      0   0
   08_BC      1     1     0     0      0   0
   12_BF      0     0     8     0      0   2
   14_BG      0     0     0     3      0   0
   15_01B     0     0     0     0      4   0
   B          0     0     3     0      0 451

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 0.643933 (all), 0.583189 (group)
Subtype Posterior Probability
01_AE 2.86852e-35
A 4.66709e-26
B 1
C 6.91547e-25
D 0.000000000024517
F 0.0000000000000745295
G 1.59474e-33
H 2.17772e-19
J 5.14486e-28
K 9.75583e-19

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    47   0   0   0   0   0   0   0   0   0
    A         0 106   0   0   0   1   0   0   2   0
    B         0   0 766   0   0   0   0   0   0   0
    C         0   0   0 497   0   0   0   0   0   0
    D         0   0   0   0  80   0   0   0   0   0
    F         0   1   0   0   0  12   0   0   0   0
    G         0   0   0   0   0   0  35   0   1   0
    H         0   0   0   1   0   0   0   6   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 nef (nested) Outlierness: 0.417848 (all), 0.65745 (group)
Subtype Posterior Probability
03_AB 1.92882e-34
07_BC 4.58618e-33
08_BC 9.80909e-45
12_BF 0.0000000115979
14_BG 7.46304e-38
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 795 at 10 Dimensional MDS
         Predicted
Objective 07_BC 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      1     5     0      0   2
   14_BG      0     0    14      0   0
   15_01B     0     0     0      4   0
   B          0     1     0      0 765

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 1.00338 (all), 1.22569 (group)
Subtype Posterior Probability
01_AE 1.0782e-36
A 1.0776e-26
B 1
C 1.37269e-16
D 2.30355e-17
F 3.43947e-20
G 2.23859e-39
H 0.000000000000170435
J 4.94186e-33
K 1.75451e-19

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 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 24  0  0  0  0  1  0  0  0
    B         0  0 62  0  0  0  0  0  0  0
    C         0  0  0 74  0  0  0  0  0  1
    D         0  0  0  0 38  0  0  0  0  0
    F         0  0  0  0  0  8  0  0  0  0
    G         0  0  0  0  0  0  9  0  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: 1.2102 (all), 1.77256 (group)
Subtype Posterior Probability
03_AB 6.7963e-43
07_BC 6.28698e-37
08_BC 2.11686e-37
12_BF 8.6354e-29
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 74 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF  B
    03_AB     2     0     0     0  0
    07_BC     0     0     2     0  0
    08_BC     0     1     4     0  0
    12_BF     0     0     0     3  0
    B         0     0     0     0 62

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