Launch prediction server Query precalculated results
Algorithms Prediction server Database query Output description Benchmark results

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 0 108 57 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.696158 (all), 1.24306 (group)
Subtype Posterior Probability
01_AE 0.0334413
A 0.00000115564
B 0.947497
C 0.00484249
D 0.000000000000173181
F 0.00547565
G 0.00873683
H 0.00000147727
J 0.00000000528225
K 0.00000422624

Cross-Validation of Discriminant Models
Miss-Classification Rate: 205 / 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   0 413  40   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: 1.12682 (all), 1.66542 (group)
Subtype Posterior Probability
01_AE 0.000525638
03_AB 0.0000522994
07_BC 0.0000170687
08_BC 0.0000628639
11_cpx 0.00000000404829
12_BF 0.000420187
13_cpx 0.0000000134108
14_BG 0.0102881
15_01B 0.00803273
B 0.980601

Cross-Validation of Discriminant Models
Miss-Classification Rate: 48 / 568 at 10 Dimensional MDS
         Predicted
Objective 01_AE 03_AB 07_BC 11_cpx 12_BF 13_cpx 15_01B   B
   01_AE     69     1     0      0     0      0      0   0
   03_AB      0     0     0      0     0      0      0   0
   07_BC      0     0     0      0     0      0      0  10
   08_BC      0     0     0      0     0      0      0   2
   11_cpx     0     0     0      9     0      1      0   1
   12_BF      0     0     0      0     0      0      0  10
   13_cpx     0     0     0      1     0      1      0   1
   14_BG      0     0     0      0     0      0      0   3
   15_01B     0     0     0      0     0      0      0   4
   B          0     3     6      1     2      0      1 441

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