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


Detailed result for env (major) Outlierness: 1.27527 (all), 1.81303 (group)
Subtype Posterior Probability
01_AE 0.00999914
A 0.00000128432
B 0.967296
C 0.00298389
D 0.0000000000608063
F 0.000810842
G 0.0188782
H 0.00000281474
J 0.0000000000740008
K 0.0000280637

Cross-Validation of Discriminant Models
Miss-Classification Rate: 204 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   J
    01_AE    68   0   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: 1.37958 (all), 1.46055 (group)
Subtype Posterior Probability
02_AG 0.00000000000000158258
03_AB 0.000230445
04_cpx 4.43687e-18
06_cpx 0.000014229
07_BC 0.0000028915
08_BC 0.00000569526
09_cpx 2.60468e-19
11_cpx 0.0000000000000121243
12_BF 0.0000253829
13_cpx 0.000000000000155436
14_BG 0.0324804
15_01B 0.000287957
B 0.966949
G 0.00000363198

Cross-Validation of Discriminant Models
Miss-Classification Rate: 83 / 589 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 07_BC 09_cpx 11_cpx 12_BF 13_cpx   B   G
   02_AG     46     0      1     0      1      6     0      0   0   1
   03_AB      0     0      0     0      0      0     0      0   0   0
   04_cpx     2     0      0     0      1      0     0      0   0   0
   06_cpx     0     0      0     0      0      0     0      0   5   1
   07_BC      0     0      0     0      0      0     0      0  10   0
   08_BC      0     0      0     0      0      0     0      0   2   0
   09_cpx     0     0      0     0      1      1     0      1   1   0
   11_cpx     5     0      0     0      1      4     0      0   0   1
   12_BF      0     0      0     0      0      0     0      0  10   0
   13_cpx     1     0      0     0      0      0     0      0   0   2
   14_BG      0     0      0     0      0      0     0      0   3   0
   15_01B     0     0      0     0      0      0     0      0   4   0
   B          0     3      0     4      0      0     2      0 445   0
   G          3     0      0     0      0      0     1      0   9  10

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