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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 210 831 246 B B B (Unambiguous Nested)
ltr 499 1022 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: 0.743643 (all), 0.861818 (group)
Subtype Posterior Probability
01_AE 1.71149e-40
A 4.13469e-32
B 1
C 9.40362e-30
D 0.000000000153335
F 3.78685e-19
G 7.07235e-42
H 1.17703e-23
J 5.07378e-36
K 1.79369e-18

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         0 108   0   0   0   0   0   0   1   0
    B         0   0 766   0   0   0   0   0   0   0
    C         1   0   0 496   0   0   0   0   0   0
    D         0   0   0   0  80   0   0   0   0   0
    F         0   0   0   0   0  11   0   1   0   1
    G         0   0   0   0   0   0  35   0   1   0
    H         0   0   0   0   0   0   1   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: 0.490967 (all), 0.614127 (group)
Subtype Posterior Probability
03_AB 1.49321e-38
07_BC 2.42552e-25
08_BC 1.05587e-33
12_BF 0.00000000000526922
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 795 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      5     0      0   3
   14_BG      0    14      0   0
   15_01B     0     0      4   0
   B          0     0      0 766

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 0.955853 (all), 1.15721 (group)
Subtype Posterior Probability
01_AE 1.15529e-35
A 6.76145e-26
B 1
C 2.04509e-16
D 1.0826e-16
F 6.93782e-20
G 3.15347e-38
H 0.00000000000080037
J 3.92657e-32
K 6.19485e-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: 1.19726 (all), 1.34671 (group)
Subtype Posterior Probability
03_AB 1.4013e-45
07_BC 4.65465e-37
08_BC 1.41601e-37
12_BF 2.29558e-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