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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 0 350 283 J J Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
4151462 AAD04425 env 0 117 97 B B B (Unambiguous Nested)


Detailed result for env (major) Outlierness: 0.884355 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 1.02666e-30
A 0.000771351
B 0.000000107663
C 0.00000000000214134
D 0.0000185611
F 0.300886
G 0.0488702
H 0.0000127908
J 0.613394
K 0.0360469

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    70   0   0   0   0   0   0   0   0
    A         0  81   1   0   0   0   0   0   0
    B         0   0 454   0   0   0   0   0   0
    C         0   0   0 463   0   0   0   0   1
    D         0   0   0   0  60   0   0   0   0
    F         0   0   0   0   0  15   1   0   0
    G         0   0   0   0   0   0  22   0   1
    H         0   0   0   0   0   1   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   1   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.910016 (all), 3.4e38 (group)
Subtype Posterior Probability
02_AG 1.25487e-16
04_cpx 1.53585e-34
05_DF 0.000000187577
06_cpx 0.000000061728
09_cpx 2.76168e-38
11_cpx 0.000000000568509
12_BF 0.00000783197
13_cpx 5.33785e-21
14_BG 0.00000000000000442563
F 0.00000759476
G 0.00000404041
J 0.999976
K 0.00000384194

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 140 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 05_DF 06_cpx 09_cpx 11_cpx 12_BF 13_cpx 14_BG  F  G  K
   02_AG     55      0     0      0      0      0     0      0     0  0  0  0
   04_cpx     1      2     0      0      0      0     0      0     0  0  0  0
   05_DF      0      0     2      0      0      0     0      0     0  1  0  0
   06_cpx     0      0     0      6      0      0     0      0     0  0  0  0
   09_cpx     0      0     0      0      4      0     0      0     0  0  0  0
   11_cpx     0      0     0      0      0     11     0      0     0  0  0  0
   12_BF      0      0     0      0      0      0     7      0     2  1  0  0
   13_cpx     1      0     0      0      0      0     0      2     0  0  0  0
   14_BG      0      0     0      0      0      0     0      0     3  0  0  0
   F          0      0     0      0      0      0     7      0     0  9  0  0
   G          0      0     0      0      0      0     0      0     0  0 23  0
   J          0      0     0      0      0      0     0      0     0  0  0  0
   K          0      0     1      0      0      0     0      0     0  0  0  1

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