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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
5tat 62 123 55 B B B B (Unambiguous Nested)
ltr 129 407 185 B B B (Unambiguous Nested)
nef 130 378 89 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 0.681563 (all), 0.886544 (group)
Subtype Posterior Probability
01_AE 0.000000000000522704
A 0.00000000101459
B 0.99999
C 0.0000000000832632
D 0.00000892036
F 0.00000059878
G 4.14388e-16
H 2.1409e-29
J 0.0000000000158287
K 0.0000000000680213

Cross-Validation of Discriminant Models
Miss-Classification Rate: 50 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    41   9   0   0   0   0   3   0   0
    A         4  53   0   3   0   0   3   0   0
    B         0   1 155   0   3   0   0   0   0
    C         0   0   0 306   1   0   0   0   0
    D         0   0   6   0  38   0   0   0   0
    F         0   0   0   2   1   9   0   0   0
    G         7   2   0   1   0   0   5   0   0
    H         0   1   0   0   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   1   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 0.773487 (all), 0.839308 (group)
Subtype Posterior Probability
03_AB 0.000254897
07_BC 3.08581e-24
08_BC 0.00000000406446
12_BF 0.000890074
14_BG 5.70792e-18
15_01B 0.0000000000000345972
B 0.998855

Cross-Validation of Discriminant Models
Miss-Classification Rate: 16 / 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     5     0      0   5
   14_BG      0     0     1      1   0
   15_01B     0     0     0      2   0
   B          1     6     0      0 152

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 0.670408 (all), 0.5762 (group)
Subtype Posterior Probability
01_AE 5.37798e-33
A 2.42754e-21
B 1
C 4.28531e-17
D 0.000000000305801
F 1.46747e-31
G 9.09617e-30
H 0.0000000000000207732
J 7.39084e-29
K 9.87771e-22

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: 0.663784 (all), 0.544905 (group)
Subtype Posterior Probability
03_AB 2.21125e-42
07_BC 2.96891e-33
08_BC 3.78239e-34
12_BF 3.16603e-35
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 nef (major) Outlierness: 0.58492 (all), 0.617893 (group)
Subtype Posterior Probability
01_AE 7.13479e-25
A 2.67857e-17
B 1
C 0.000000000000078899
D 0.0000000101387
F 0.0000000000000211877
G 2.14122e-24
H 0.000000000000191235
J 3.57919e-28
K 4.57747e-20

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    46   0   0   0   0   0   0   0   1   0
    A         0 107   0   1   0   0   0   1   0   0
    B         0   0 764   0   1   0   1   0   0   0
    C         0   0   1 495   0   0   1   0   0   0
    D         0   0   3   0  77   0   0   0   0   0
    F         0   0   2   3   0   8   0   0   0   0
    G         0   0   0   0   0   0  35   0   1   0
    H         0   0   0   3   0   0   0   4   0   0
    J         1   0   0   0   0   0   0   0   0   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: 0.454426 (all), 0.429804 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 7.53573e-16
14_BG 4.62435e-30
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


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