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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
ltr 1 632 256 B B B B (Unambiguous Nested)
gag 791 2294 963 B B B (Unambiguous Nested)
pol 2086 5098 2703 B B B (Unambiguous Nested)
vif 5042 5621 522 B B B (Unambiguous Nested)
vpr 5560 5851 147 B B B (Unambiguous Nested)
5tat 5831 6042 185 B B B (Unambiguous Nested)
vpu 6075 6308 95 B B B (Major agrees Nested with high confidence)
env 6225 8796 1588 B B B (Unambiguous Nested)
nef 8797 9430 246 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
221475 BAA00996 tat 0 101 94 B B B (Unambiguous Nested)


Detailed result for ltr (major) Outlierness: 0.919722 (all), 1 (group)
Subtype Posterior Probability
01_AE 4.694e-37
A 2.36291e-17
B 1
C 1.13294e-24
D 1.17361e-17
F 1.32532e-16
G 3.1026e-40
H 0.00000000000925263
J 1.50512e-34
K 4.00938e-21

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 (all), 1 (group)
Subtype Posterior Probability
03_AB 2.51211e-41
07_BC 1.67867e-38
08_BC 4.04258e-39
12_BF 6.67644e-27
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


Detailed result for gag (major) Outlierness: 0.581423 (all), 0.739023 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 7.06558e-23
F 0
G 0
H 4.49817e-42
J 1.33681e-29
K 1.33643e-36

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    72   0   0   0   0   0   0   0   0
    A         0 129   0   1   0   0   1   2   0
    B         0   0 262   0   1   2   0   0   0
    C         0   0   0 552   0   0   0   1   0
    D         0   0   0   0  76   0   0   0   0
    F         0   0   0   0   0  14   0   0   1
    G         0   0   0   0   0   0  21   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   3

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.319218 (all), 0.475609 (group)
Subtype Posterior Probability
03_AB 0
07_BC 3.70753e-38
08_BC 0
12_BF 4.04899e-18
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      3     0     0      0   0
   08_BC      0     5     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     2      0 263

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (major) Outlierness: 0.736921 (all), 0.944499 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 3.80733e-42
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         0  58   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0  11   0   0   1
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   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: 0.478013 (all), 0.659029 (group)
Subtype Posterior Probability
03_AB 0.0000804749
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 0.99992

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 184 at 10 Dimensional MDS
         Predicted
Objective 12_BF 15_01B   B
   03_AB      0      0   0
   07_BC      0      0   0
   08_BC      0      0   0
   12_BF      9      0   0
   14_BG      0      0   0
   15_01B     0      3   0
   B          0      0 168

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 0.731015 (all), 0.617329 (group)
Subtype Posterior Probability
01_AE 0
A 1.0762e-41
B 1
C 0
D 8.56809e-22
F 2.52234e-44
G 4.89765e-40
H 7.21395e-20
J 7.09808e-25
K 5.8076e-25

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 945 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    53   0   0   0   0   0   0   0   0
    A         0  70   0   0   0   0   4   0   0
    B         0   0 370   0   0   0   0   0   0
    C         0   0   0 364   0   0   0   0   0
    D         0   0   0   0  47   0   0   1   0
    F         0   0   0   0   0  10   0   3   0
    G         0   1   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   2   1
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 0.921109 (all), 0.933508 (group)
Subtype Posterior Probability
03_AB 0.000000219939
12_BF 0
14_BG 1.4013e-45
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 386 at 10 Dimensional MDS
         Predicted
Objective 03_AB 12_BF 14_BG 15_01B   B
   03_AB      0     0     0      0   0
   12_BF      0     9     0      0   0
   14_BG      0     0     3      0   0
   15_01B     0     0     0      3   0
   B          1     0     0      0 369

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (major) Outlierness: 1 (all), 1 (group)
Subtype Posterior Probability
01_AE 1.1056e-19
A 9.18073e-22
B 1
C 1.39371e-18
D 0.000000000105055
F 0.000000000000622295
G 1.33837e-21
H 0.0000000000000548534
J 2.49429e-16
K 0.00000000000000494198

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 810 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    31   0   0   0   0   0   0   0   0
    A         1  55   0   0   0   0   0   0   0
    B         0   0 283   0   1   0   0   1   0
    C         0   0   0 364   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0
    F         0   0   0   0   0   9   0   0   0
    G         1   0   0   0   0   0  14   0   0
    H         0   0   0   0   0   1   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 vpr (nested) Outlierness: 1 (all), 1 (group)
Subtype Posterior Probability
03_AB 0.0000825787
07_BC 0.000000000262928
08_BC 5.11067e-29
12_BF 0.000000000452706
14_BG 4.39007e-24
15_01B 3.25231e-37
B 0.999917

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 300 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      0     6     0      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     2      1   0
   B          1     1     0      0 283

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.599685 (all), 0.862742 (group)
Subtype Posterior Probability
01_AE 1.47234e-27
A 4.88614e-19
B 1
C 1.79789e-25
D 0.000000000188884
F 8.48188e-16
G 7.42241e-21
H 5.81842e-28
J 0.00000000000000425853
K 2.33643e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    52   1   0   0   0   0   0   0   0   0
    A         2  58   1   0   0   0   2   0   0   0
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   0   0  44   0   0   0   0   0
    F         0   0   0   0   0  10   0   0   0   2
    G         1   0   0   0   0   0  14   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 0.331027 (all), 0.582266 (group)
Subtype Posterior Probability
03_AB 0.000503304
07_BC 4.98663e-16
08_BC 2.22949e-23
12_BF 0.000000262129
14_BG 2.26675e-19
15_01B 9.10948e-25
B 0.999496

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 176 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      7     0      0   3
   14_BG      0     2      0   0
   15_01B     0     0      2   0
   B          0     0      0 159

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.698916 (all), 0.698315 (group)
Subtype Posterior Probability
01_AE 0.0000000000000270559
A 0.00000000000000798265
B 0.999999
C 1.3074e-19
D 0.00000107122
F 0.000000000023521
G 0.0000000120425
H 0.00000000000000127975
J 2.1258e-29
K 7.44048e-22

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 932 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    44   2   0   0   0   0   0   0   0
    A         3  64   1   0   0   0   0   2   0
    B         0   0 321   0   0   0   0   0   0
    C         0   0   0 397   0   0   0   0   0
    D         0   0   0   0  54   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  22   0   0
    H         0   3   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   2
    K         0   0   0   0   0   1   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (nested) Outlierness: 0.894644 (all), 1 (group)
Subtype Posterior Probability
03_AB 0.000112705
08_BC 6.26243e-22
12_BF 0.031482
14_BG 4.58329e-23
15_01B 0.00000000000000657761
B 0.968405

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 340 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     0      0  12
   14_BG      0     3      0   0
   15_01B     0     0      2   0
   B          1     0      0 320

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 0.813203 (all), 0.979591 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 0
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 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         0  82   0   0   0   0   0   0   0
    B         0   0 454   0   0   0   0   0   0
    C         0   0   0 464   0   0   0   0   0
    D         0   0   0   0  60   0   0   0   0
    F         0   0   0   0   0  15   0   0   1
    G         0   0   0   0   0   0  23   0   0
    H         0   0   0   0   0   0   0   3   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 env (nested) Outlierness: 0.868963 (all), 0.873712 (group)
Subtype Posterior Probability
03_AB 0.000092447
07_BC 0
08_BC 0
12_BF 1.02845e-29
14_BG 0.00000000000000113156
15_01B 0.00000000000584572
B 0.999908

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 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      7     3     0     0      0   0
   08_BC      2     0     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     0     0     10 444

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 0.566073 (all), 0.450562 (group)
Subtype Posterior Probability
01_AE 3.10948e-42
A 5.55735e-24
B 1
C 6.20542e-32
D 0.00000000005148
F 2.99358e-18
G 0
H 3.17222e-25
J 3.27943e-36
K 5.14602e-22

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: 0.499094 (all), 0.552192 (group)
Subtype Posterior Probability
03_AB 2.57728e-40
07_BC 8.36814e-24
08_BC 9.57979e-33
12_BF 0.000000000000237576
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


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea