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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 537 1646 784 ? B B B (Unambiguous Nested)
pol 1438 4450 2666 B B B (Major agrees Nested with high confidence)
vif 4394 4973 522 B B B (Unambiguous Nested)
vpr 4912 5203 147 B B B (Unambiguous Nested)
5tat 5183 5394 185 B B B (Unambiguous Nested)
vpu 5427 5660 95 B B B (Major agrees Nested with high confidence)
env 5577 7925 1455 B 14_BG Undecided


Detailed result for gag (major) Outlierness: 0.86926 (all), 1.24956 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 5.80781e-23
F 7.00649e-45
G 0
H 3.13195e-35
J 7.12286e-26
K 2.0294e-37

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 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         0 130   0   1   0   0   1   1   0
    B         0   0 262   0   1   2   0   0   0
    C         0   0   0 552   0   0   0   0   1
    D         0   0   0   0  76   0   0   0   0
    F         0   0   0   0   0  12   0   0   3
    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: 1.17027 (all), 1.42236 (group)
Subtype Posterior Probability
03_AB 0
07_BC 4.68034e-43
08_BC 5.92413e-39
12_BF 4.12353e-20
14_BG 0
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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     9      0   1
   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: 1.08976 (all), 1.25867 (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 / 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  12   0   0   0
    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: 3.30283 (all), 3.74228 (group)
Subtype Posterior Probability
03_AB 0.000000000000295351
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 1

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: 0.746482 (all), 1.12085 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 8.40779e-45
D 6.80666e-29
F 1.70958e-43
G 1.4013e-45
H 1.60225e-23
J 3.84665e-28
K 4.18627e-27

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: 1.04136 (all), 1.1134 (group)
Subtype Posterior Probability
03_AB 0.0000017287
12_BF 3.38778e-41
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: 0.900684 (all), 0.958049 (group)
Subtype Posterior Probability
01_AE 2.99152e-17
A 5.25639e-19
B 1
C 9.49145e-19
D 0.000000120946
F 0.000000000118348
G 6.5909e-22
H 0.0000000000209832
J 0.000000000000028249
K 0.00000000000000347988

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: 0.610814 (all), 0.588428 (group)
Subtype Posterior Probability
03_AB 0.00075106
07_BC 0.00000000274101
08_BC 6.15928e-27
12_BF 0.00000000726717
14_BG 2.60919e-22
15_01B 5.62313e-36
B 0.999249

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: 0.774455 (all), 1.16982 (group)
Subtype Posterior Probability
01_AE 1.23133e-32
A 2.4917e-23
B 1
C 2.13207e-36
D 0.0000000000145134
F 3.53366e-26
G 2.28296e-23
H 2.49042e-34
J 3.49082e-24
K 2.34177e-26

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: 0.73152 (all), 0.718709 (group)
Subtype Posterior Probability
03_AB 0.0000261065
07_BC 0.00000000000000273798
08_BC 9.75409e-23
12_BF 0.00000000000683063
14_BG 1.39403e-21
15_01B 2.00598e-27
B 0.999974

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 176 at 10 Dimensional MDS
         Predicted
Objective 03_AB 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     7     0      0   3
   14_BG      0     0     2      0   0
   15_01B     0     0     0      2   0
   B          1     0     0      0 158

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.550983 (all), 0.643275 (group)
Subtype Posterior Probability
01_AE 0.0000000014657
A 0.00000000122915
B 0.999993
C 0.000000000000162561
D 0.00000734102
F 0.0000000246711
G 0.00000000000946632
H 0.0000000000119057
J 2.39464e-23
K 5.29113e-24

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: 0.718451 (all), 0.712239 (group)
Subtype Posterior Probability
03_AB 0.0000502353
08_BC 2.19943e-19
12_BF 0.0165176
14_BG 1.08389e-35
15_01B 0.0000000000000484101
B 0.983432

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: 4.93496 (all), 13.7949 (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: 12.0594 (all), 84.263 (group)
Subtype Posterior Probability
03_AB 4.52801e-34
07_BC 0
08_BC 0
12_BF 0
14_BG 0.999959
15_01B 2.94052e-29
B 0.00004144

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      7     3     0      0   0
   08_BC      2     0     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   3
   15_01B     0     0     0      4   0
   B          0     0     0     10 444

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