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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 13 628 246 B B B B (Unambiguous Nested)
ltr 296 628 256 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60116 CAA44766 nef 11 121 51 B B B (Unambiguous Nested)


Detailed result for nef (major) Outlierness: 0.848312 (all), 0.897754 (group)
Subtype Posterior Probability
01_AE 0
A 1.87005e-31
B 1
C 8.31254e-40
D 0.00000000000603103
F 2.99976e-25
G 0
H 3.89319e-33
J 0
K 2.84664e-30

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: 0.764082 (all), 0.796469 (group)
Subtype Posterior Probability
03_AB 0
07_BC 2.79422e-27
08_BC 2.78169e-38
12_BF 6.03886e-16
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: 1.04416 (all), 1.2984 (group)
Subtype Posterior Probability
01_AE 0
A 4.76649e-26
B 1
C 3.69195e-31
D 2.62054e-17
F 2.35267e-26
G 0
H 6.9167e-20
J 1.96182e-44
K 7.61546e-31

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: 0.789808 (all), 0.82557 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 4.1732e-37
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


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