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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 1021 256 B B B (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.825777 (all), 0.699957 (group)
Subtype Posterior Probability
01_AE 8.51507e-35
A 9.68826e-22
B 0.999999
C 7.81722e-30
D 0.00000115693
F 0.000000000000817376
G 0.00000000000000191678
H 0.0000000000163472
J 5.99872e-21
K 0.00000000000000457505

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: 0.765396 (all), 0.701337 (group)
Subtype Posterior Probability
03_AB 8.52058e-16
07_BC 1.19225e-35
08_BC 0
12_BF 0.000250453
14_BG 2.17242e-40
15_01B 8.5665e-39
B 0.99975

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: 0.677369 (all), 0.795318 (group)
Subtype Posterior Probability
01_AE 2.18924e-39
A 1.07304e-30
B 1
C 3.48242e-29
D 0.000000000253576
F 9.95108e-19
G 1.01349e-40
H 7.97158e-23
J 5.29941e-35
K 2.27823e-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: 0.438019 (all), 0.625767 (group)
Subtype Posterior Probability
03_AB 1.67397e-37
07_BC 7.34714e-25
08_BC 3.92454e-33
12_BF 0.00000000000810375
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