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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
gag 0 200 126 B 14_BG Undecided


Detailed result for gag (major) Outlierness: 0.724688 (all), 2.11331 (group)
Subtype Posterior Probability
01_AE 0.000000856255
A 0.000000390586
B 0.823173
C 0.0000000495256
D 0.000395346
F 0.00000000000000211558
G 0.176429
H 0.00000107172
J 0.0000000192441
K 0.0000000000000131795

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    71   1   0   0   0   0   0   0   0
    A         3 128   0   1   0   0   1   0   0
    B         0   0 262   0   1   2   0   0   0
    C         0   0   1 549   0   0   0   0   3
    D         0   0   4   0  72   0   0   0   0
    F         0   0   0   0   0  14   0   0   1
    G         0   0   1   0   0   0  20   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   2   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 1.12542 (all), 3.4e38 (group)
Subtype Posterior Probability
02_AG 5.74944e-30
03_AB 7.55439e-33
04_cpx 1.78296e-17
06_cpx 1.01902e-32
07_BC 9.78962e-16
08_BC 2.1549e-20
09_cpx 3.01489e-19
11_cpx 0.00000000000000326302
12_BF 9.38414e-19
13_cpx 0.00624839
14_BG 0.993487
15_01B 6.52702e-20
B 0.00000265682
G 0.00026216

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 400 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 07_BC 08_BC 09_cpx 11_cpx 12_BF 13_cpx 14_BG
   02_AG     57      1      0     0     0      0      0     0      0     0
   03_AB      0      0      0     0     0      0      0     0      0     0
   04_cpx     0      0      0     0     0      2      0     0      0     0
   06_cpx     0      0      9     0     0      0      0     0      0     0
   07_BC      0      0      0     2     1      0      0     0      0     0
   08_BC      0      0      0     1     4      0      0     0      0     0
   09_cpx     0      1      0     0     0      4      0     0      0     0
   11_cpx     0      0      0     0     0      1      9     0      0     0
   12_BF      0      0      0     0     0      0      0     8      0     0
   13_cpx     0      0      0     0     0      0      0     0      1     0
   14_BG      0      0      0     0     0      0      0     0      0     0
   15_01B     0      0      0     0     0      0      0     0      0     0
   B          0      0      0     0     0      0      0     2      0     0
   G          0      0      0     0     0      0      0     0      3     2
         Predicted
Objective 15_01B   B   G
   02_AG       1   0   0
   03_AB       0   0   0
   04_cpx      1   0   0
   06_cpx      0   0   0
   07_BC       0   0   0
   08_BC       0   0   0
   09_cpx      0   0   0
   11_cpx      0   0   0
   12_BF       0   2   0
   13_cpx      0   0   2
   14_BG       0   0   0
   15_01B      5   0   0
   B           0 263   0
   G           0   0  16

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