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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
pol 0 213 198 J J Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
51895748 AAU13904 pol 0 71 67 J J Undecided


Detailed result for pol (major) Outlierness: 0.273828 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.00000000000000304981
A 0.0000389088
B 0.0802947
C 0.000876985
D 0.0675238
F 0.000000819901
G 0.00512821
H 0.00000465679
J 0.84412
K 0.00201217

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         1  57   0   1   0   0   0   0   0
    B         0   0 167   0   0   0   0   0   1
    C         0   0   1 369   0   0   1   0   0
    D         0   0   1   0  45   0   0   0   0
    F         0   0   0   0   0  11   0   1   0
    G         0   2   1   0   0   0  12   1   0
    H         0   0   0   0   0   0   1   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   1   0   0   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.778656 (all), 3.4e38 (group)
Subtype Posterior Probability
03_AB 0.000000000000105727
05_DF 0.000000379156
06_cpx 0.0000000000000157224
07_BC 1.70666e-36
08_BC 3.64338e-44
10_CD 0.0000000062397
11_cpx 0.00000000371252
12_BF 0.000000053444
13_cpx 0.00000083627
14_BG 0.00000124178
15_01B 4.8807e-37
16_A2D 0.00000000000151383
B 0.000026609
D 0.000000419395
J 0.99997

Cross-Validation of Discriminant Models
Miss-Classification Rate: 26 / 257 at 10 Dimensional MDS
         Predicted
Objective 05_DF 06_cpx 07_BC 10_CD 11_cpx 12_BF 13_cpx 15_01B 16_A2D   B   D
   03_AB      0      0     0     0      0     0      0      0      0   0   0
   05_DF      1      0     0     0      0     0      0      0      0   0   2
   06_cpx     0      5     0     0      0     0      0      0      0   0   0
   07_BC      0      0     0     0      0     0      0      0      0   0   0
   08_BC      0      0     0     0      0     0      0      0      0   0   0
   10_CD      0      0     0     0      0     0      0      0      0   0   3
   11_cpx     0      0     0     0      9     0      1      0      0   0   0
   12_BF      0      0     0     0      0     5      0      0      0   4   0
   13_cpx     0      0     0     0      1     0      2      0      0   0   0
   14_BG      0      0     0     0      0     0      0      0      0   0   0
   15_01B     0      0     0     0      0     0      0      3      0   0   0
   16_A2D     0      0     0     0      0     0      1      0      1   0   0
   B          0      0     1     0      0     3      0      0      0 164   0
   D          2      0     0     1      0     0      0      0      0   1  41
   J          0      0     0     0      0     0      0      0      0   0   0
         Predicted
Objective   J
   03_AB    0
   05_DF    0
   06_cpx   0
   07_BC    0
   08_BC    0
   10_CD    0
   11_cpx   0
   12_BF    0
   13_cpx   0
   14_BG    0
   15_01B   0
   16_A2D   0
   B        0
   D        1
   J        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