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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 58 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.857479 (all), 1.10493 (group)
Subtype Posterior Probability
01_AE 0.000589467
A 0.000000124808
B 0.980428
C 0.00432679
D 0.000000000797124
F 0.00335767
G 0.011293
H 0.00000025021
J 0.000000000258556
K 0.00000436816

Cross-Validation of Discriminant Models
Miss-Classification Rate: 219 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    68   0   2   0   0   0   0   0   0
    A         0  75   0   2   0   1   1   1   2
    B         0   0 410  40   4   0   0   0   0
    C         0   4 106 352   1   0   1   0   0
    D         0   0   8   5  46   0   0   0   1
    F         0   0   8   8   0   0   0   0   0
    G         0   2  10   6   0   0   5   0   0
    H         0   2   0   0   0   0   1   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.866627 (all), 0.882044 (group)
Subtype Posterior Probability
02_AG 0.0000000000000156282
03_AB 0.000000276093
04_cpx 0.0000000000000376063
06_cpx 0.00000358189
07_BC 0.000104082
08_BC 0.000021059
09_cpx 0.000000000000001412
11_cpx 0.0000000000110162
12_BF 0.000455346
13_cpx 0.0000000000645918
14_BG 0.125587
15_01B 0.00134955
B 0.872431
G 0.0000473265

Cross-Validation of Discriminant Models
Miss-Classification Rate: 72 / 589 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 07_BC 09_cpx 11_cpx 12_BF 13_cpx   B   G
   02_AG     48     0      1      0     0      1      4     0      0   0   1
   03_AB      0     0      0      0     0      0      0     0      0   0   0
   04_cpx     2     0      0      0     0      0      0     0      1   0   0
   06_cpx     0     0      0      1     0      0      0     0      0   0   5
   07_BC      0     0      0      0     0      0      0     0      0  10   0
   08_BC      0     0      0      0     0      0      0     0      0   2   0
   09_cpx     0     0      0      0     0      1      1     0      1   1   0
   11_cpx     4     0      0      0     0      0      6     0      0   0   1
   12_BF      0     0      0      0     0      0      0     0      0  10   0
   13_cpx     1     0      0      0     0      0      1     0      0   0   1
   14_BG      0     0      0      0     0      0      0     0      0   3   0
   15_01B     0     0      0      0     0      0      0     0      0   4   0
   B          0     1      0      0     1      0      0     1      0 450   1
   G          3     0      0      0     0      0      0     2      0   7  11

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