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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
gag 114 1617 963 ? B B B (Unambiguous Nested)
pol 1409 4421 2703 B B B (Unambiguous Nested)
vif 4365 4944 522 B B B (Unambiguous Nested)
vpr 4883 5174 147 B B B (Unambiguous Nested)
5tat 5154 5365 185 B B B (Unambiguous Nested)
vpu 5398 5631 95 B B B (Unambiguous Nested)
env 5548 7994 1533 B B Undecided


Detailed result for gag (major) Outlierness: 0.879633 (all), 1.39582 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 4.79094e-30
F 0
G 0
H 0
J 0
K 0

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: 1.1155 (all), 1.13225 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 2.09362e-20
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: 0.888448 (all), 1.17019 (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: 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: 0.93049 (all), 0.922507 (group)
Subtype Posterior Probability
03_AB 0.00000142345
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 0.999999

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: 0.740495 (all), 0.950412 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.54982e-19
F 0
G 7.00649e-45
H 1.07116e-27
J 7.40695e-31
K 1.54517e-30

Cross-Validation of Discriminant Models
Miss-Classification Rate: 14 / 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   1   2
    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: 0.866557 (all), 1.34362 (group)
Subtype Posterior Probability
03_AB 0.00000157632
12_BF 0
14_BG 0
15_01B 0
B 0.999998

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: 0.744743 (all), 0.749876 (group)
Subtype Posterior Probability
01_AE 0.00000000000000675146
A 4.56003e-20
B 1
C 0.000000000000156843
D 0.000000000146126
F 0.0000000000101095
G 4.98232e-17
H 0.00000000000336318
J 0.0000000000142712
K 3.57168e-16

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: 0.739831 (all), 0.669839 (group)
Subtype Posterior Probability
03_AB 0.000168862
07_BC 0.0000000000000976332
08_BC 1.81706e-26
12_BF 0.0000000878815
14_BG 0.00000000000000415157
15_01B 1.74124e-25
B 0.999831

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: 0.746805 (all), 0.777622 (group)
Subtype Posterior Probability
01_AE 1.36563e-36
A 2.68012e-26
B 1
C 7.29589e-34
D 0.000000000000117359
F 3.97157e-23
G 5.22104e-27
H 6.22787e-37
J 2.80942e-21
K 4.45159e-24

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: 1.16169 (all), 1.11802 (group)
Subtype Posterior Probability
03_AB 0.00000688301
07_BC 4.86074e-19
08_BC 1.13019e-20
12_BF 0.000000000429264
14_BG 2.16973e-21
15_01B 2.09884e-29
B 0.999993

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: 0.888238 (all), 0.889989 (group)
Subtype Posterior Probability
01_AE 0.00000000000000228145
A 3.28107e-16
B 1
C 0.00000000000000110183
D 0.000000000625978
F 0.00000000000000524069
G 0.000000000000605461
H 0.0000000000000307447
J 6.76832e-26
K 2.90854e-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: 0.962278 (all), 1.00021 (group)
Subtype Posterior Probability
03_AB 0.0000173563
08_BC 2.04364e-24
12_BF 0.00036557
14_BG 2.25827e-23
15_01B 7.30327e-18
B 0.999617

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: 4.02112 (all), 11.0212 (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: 17.1923 (all), 19.3523 (group)
Subtype Posterior Probability
03_AB 0.00000000000574978
07_BC 0
08_BC 0
12_BF 0
14_BG 0.00000000000000130509
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 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     2      0   1
   15_01B     0     0     0     0      4   0
   B          0     0     0     3      9 442

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