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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 11 644 246 B B B B (Unambiguous Nested)
ltr 312 662 256 B B B (Unambiguous Nested)


Detailed result for nef (major) Outlierness: 0.80412 (all), 0.864706 (group)
Subtype Posterior Probability
01_AE 0
A 2.28815e-34
B 1
C 1.54905e-32
D 0.00000000000188521
F 1.40724e-20
G 0
H 2.87156e-29
J 4.21791e-43
K 1.1322e-24

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: 0.854719 (all), 0.894607 (group)
Subtype Posterior Probability
03_AB 0
07_BC 1.01126e-27
08_BC 4.53298e-38
12_BF 0.0000000000000218002
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


Detailed result for ltr (major) Outlierness: 0.874214 (all), 1.26394 (group)
Subtype Posterior Probability
01_AE 6.39186e-31
A 5.01019e-21
B 1
C 7.88717e-16
D 0.00000000000000131282
F 1.16569e-22
G 4.55321e-40
H 0.0000000000000144044
J 2.00377e-27
K 4.19466e-16

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: 1.0372 (all), 1.15648 (group)
Subtype Posterior Probability
03_AB 0
07_BC 9.72419e-38
08_BC 1.91948e-36
12_BF 4.39939e-35
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 74 at 10 Dimensional MDS
         Predicted
Objective 03_AB 08_BC 12_BF  B
    03_AB     2     0     0  0
    07_BC     0     2     0  0
    08_BC     0     5     0  0
    12_BF     0     0     3  0
    B         0     0     0 62

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