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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 11 181 64 B B B B (Major agrees Nested with high confidence)


Detailed result for nef (major) Outlierness: 0.420977 (all), 0.573299 (group)
Subtype Posterior Probability
01_AE 0.00000000000000307631
A 0.000000000000789214
B 0.858221
C 0.000000000226305
D 0.141775
F 0.000000000805521
G 5.47588e-23
H 3.5166e-16
J 3.32471e-16
K 0.00000475587

Cross-Validation of Discriminant Models
Miss-Classification Rate: 72 / 1559 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    46   1   0   0   0   0   0   0   0   0
    A        11  93   0   3   0   0   2   0   0   0
    B         0   0 752   0  10   2   0   0   0   2
    C         2   3   1 485   0   1   4   1   0   0
    D         0   0  21   0  59   0   0   0   0   0
    F         0   0   1   1   0  11   0   0   0   0
    G         0   0   1   1   0   0  34   0   0   0
    H         0   1   0   0   0   0   0   6   0   0
    J         0   1   0   0   0   0   0   0   1   0
    K         0   0   2   0   0   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (nested) Outlierness: 0.412006 (all), 0.382323 (group)
Subtype Posterior Probability
03_AB 1.0644e-39
05_DF 5.40428e-19
07_BC 0.0000131506
08_BC 0.00000499184
10_CD 0.0000000490456
12_BF 0.000000000237379
14_BG 5.47948e-25
15_01B 1.90844e-20
16_A2D 0
B 0.953244
D 0.0467382

Cross-Validation of Discriminant Models
Miss-Classification Rate: 56 / 883 at 10 Dimensional MDS
         Predicted
Objective 05_DF 07_BC 08_BC 10_CD 12_BF 14_BG 15_01B 16_A2D   B   D
   03_AB      0     0     0     0     0     0      0      0   0   0
   05_DF      0     0     0     0     3     0      0      0   0   0
   07_BC      0     0     0     0     0     0      0      0   0   0
   08_BC      0     0     0     0     0     0      0      0   0   0
   10_CD      0     0     0     0     0     1      0      0   0   2
   12_BF      2     0     0     0     4     0      0      0   2   0
   14_BG      0     0     0     1     0    13      0      0   0   0
   15_01B     0     0     0     0     0     0      4      0   0   0
   16_A2D     0     0     0     0     0     1      0      1   0   0
   B          0     1     4     1     4     0      1      0 743  12
   D          0     0     0     0     0     0      1      0  17  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