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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
nef 0 332 139 ? B B B (Unambiguous Nested)
ltr 0 629 256 B B B (Unambiguous Nested)
gag 787 2290 963 B B B (Unambiguous Nested)
pol 2082 2438 251 B B B (Unambiguous Nested)
5tat 2525 2736 185 B B B (Unambiguous Nested)
vpu 2769 3003 95 B B B (Major agrees Nested with high confidence)
env 2920 5521 1588 B B B (Unambiguous Nested)


Detailed result for nef (major) Outlierness: 0.767592 (all), 0.939294 (group)
Subtype Posterior Probability
01_AE 7.15301e-31
A 2.32582e-18
B 1
C 8.13978e-19
D 0.0000000000000415459
F 0.0000000000000027806
G 7.36718e-25
H 0.00000000000000207949
J 5.26482e-26
K 1.06137e-22

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 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   1   0   0
    B         0   0 766   0   0   0   0   0   0   0
    C         0   0   1 495   0   0   0   1   0   0
    D         0   0   2   0  78   0   0   0   0   0
    F         0   0   2   0   0  10   0   0   1   0
    G         0   0   0   0   0   0  35   0   0   1
    H         0   0   0   3   0   0   0   4   0   0
    J         0   0   0   0   0   0   0   0   1   1
    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: 0.514296 (all), 0.796185 (group)
Subtype Posterior Probability
03_AB 1.46678e-22
07_BC 7.44122e-37
08_BC 1.35935e-38
12_BF 0.00000000000286635
14_BG 9.75812e-25
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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      6     0      0   2
   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: 0.665298 (all), 0.455735 (group)
Subtype Posterior Probability
01_AE 7.06078e-34
A 4.1235e-20
B 1
C 5.0775e-23
D 2.56116e-21
F 1.71375e-24
G 3.67518e-32
H 0.0000000000000020005
J 3.92007e-32
K 8.10777e-20

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: 0.482888 (all), 0.543644 (group)
Subtype Posterior Probability
03_AB 2.43381e-37
07_BC 4.09708e-34
08_BC 2.34196e-34
12_BF 2.38177e-32
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: 0.640969 (all), 0.307151 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 1.16856e-20
F 1.13371e-40
G 0
H 7.00649e-44
J 3.30782e-29
K 3.67675e-35

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: 0.435059 (all), 0.27437 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 7.14803e-17
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: 0.714658 (all), 0.812833 (group)
Subtype Posterior Probability
01_AE 0.00000000000125219
A 0.0000000000000678135
B 0.999782
C 6.20361e-16
D 0.000217553
F 0.0000000000022128
G 3.56445e-20
H 0.000000000000252996
J 0.00000000132609
K 0.000000000000536072

Cross-Validation of Discriminant Models
Miss-Classification Rate: 29 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    55   2   0   0   0   0   0   0   0   0
    A         6  52   0   0   0   0   0   1   0   0
    B         0   0 161   0   2   4   0   0   1   0
    C         0   0   0 369   2   0   0   0   0   0
    D         1   2   1   0  42   0   0   0   0   0
    F         0   0   0   0   0  11   0   0   0   1
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   1   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   1   0   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.404786 (all), 0.414881 (group)
Subtype Posterior Probability
03_AB 1.19962e-18
07_BC 0.0000106961
08_BC 1.51912e-20
12_BF 0.00000000173334
14_BG 1.15962e-25
15_01B 5.80798e-20
B 0.999989

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 184 at 10 Dimensional MDS
         Predicted
Objective 07_BC 12_BF 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     9      0   0
   14_BG      0     0      0   0
   15_01B     0     0      3   0
   B          1     3      0 164

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.656025 (all), 1 (group)
Subtype Posterior Probability
01_AE 9.22092e-31
A 6.59466e-22
B 1
C 1.1572e-29
D 2.13434e-16
F 4.62107e-26
G 1.53012e-22
H 5.27361e-35
J 2.53417e-20
K 1.0385e-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: 0.648561 (all), 0.862715 (group)
Subtype Posterior Probability
03_AB 0.00200223
07_BC 0.00000000000643866
08_BC 5.2818e-21
12_BF 0.0000000024165
14_BG 7.15042e-20
15_01B 3.94347e-27
B 0.997998

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: 0.476557 (all), 0.632817 (group)
Subtype Posterior Probability
01_AE 0.000000000000173321
A 0.00000000000062927
B 1
C 0.00000000000599346
D 0.0000000346197
F 0.0000000000615227
G 0.00000000000294258
H 0.0000000000000296662
J 5.30224e-26
K 8.05238e-23

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: 0.542832 (all), 0.551683 (group)
Subtype Posterior Probability
03_AB 0.0000736372
08_BC 1.21666e-17
12_BF 0.0302265
14_BG 2.3435e-26
15_01B 0.0000000000000312397
B 0.9697

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: 0.864416 (all), 0.664667 (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: 0.565618 (all), 0.593365 (group)
Subtype Posterior Probability
03_AB 0.00194492
07_BC 0
08_BC 0
12_BF 5.35961e-37
14_BG 1.49851e-16
15_01B 0.000000000000765137
B 0.998055

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


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