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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
env 0 102 57 H 06_cpx Undecided


Detailed result for env (major) Outlierness: 1.23324 (all), 21.0945 (group)
Subtype Posterior Probability
01_AE 0.0000000289664
A 0.0468901
B 0.0021235
C 0.000129694
D 1.95245e-18
F 0.0005024
G 0.0935025
H 0.461925
J 0.394899
K 0.0000279869

Cross-Validation of Discriminant Models
Miss-Classification Rate: 206 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   J
    01_AE    67   1   2   0   0   0   0   0
    A         0  78   1   1   0   1   0   1
    B         0   0 412  41   1   0   0   0
    C         0   4 103 356   1   0   0   0
    D         0   0   7   3  50   0   0   0
    F         0   0   7   9   0   0   0   0
    G         0   2  11   4   0   0   6   0
    H         0   2   0   0   0   0   1   0
    J         0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 1.49146 (all), 4.46278 (group)
Subtype Posterior Probability
02_AG 0.0000000144259
03_AB 0.0000027575
04_cpx 0.0000000000161791
06_cpx 0.996375
09_cpx 0.000000000418884
11_cpx 0.00000368069
13_cpx 0.000000394476
14_BG 0.0000000264888
16_A2D 9.20499e-16
A 0.0000000141473
G 0.000137063
H 0.0000000389412
J 0.00348063

Cross-Validation of Discriminant Models
Miss-Classification Rate: 87 / 197 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 14_BG  A  G  H  J
   02_AG     22      0      0      0      1     0 31  0  1  0
   03_AB      0      0      0      0      0     0  0  0  0  0
   04_cpx     2      0      0      1      0     0  0  0  0  0
   06_cpx     0      0      5      0      0     0  0  1  0  0
   09_cpx     1      1      0      0      0     1  1  0  0  0
   11_cpx     1      0      0      0      0     0 10  0  0  0
   13_cpx     0      0      0      0      0     0  3  0  0  0
   14_BG      0      0      0      0      0     2  0  1  0  0
   16_A2D     0      0      0      0      0     0  1  1  0  0
   A         13      0      0      1      1     0 63  1  2  1
   G          0      0      1      0      0     1  3 18  0  0
   H          1      0      0      0      0     0  2  0  0  0
   J          0      0      0      0      0     0  0  0  0  0

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