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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
5tat 0 144 124 H H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693985 AAP33775 tat 0 86 79 D D D (Major agrees Nested with high confidence)


Detailed result for 5tat (major) Outlierness: 2.08929 (all), 31.8709 (group)
Subtype Posterior Probability
01_AE 0.000000210393
A 0.0184435
B 1.61981e-27
C 0.0000809269
D 0.000000000096526
F 4.45304e-24
G 0.000000000327086
H 0.878598
J 0.000000215169
K 0.102877

Cross-Validation of Discriminant Models
Miss-Classification Rate: 19 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    52   0   0   0   0   0   1   0   0   0
    A         6  52   1   1   0   1   1   0   0   1
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   2   9   0   1   0   0
    G         0   0   0   0   0   0  15   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 4.49172 (all), 23.8932 (group)
Subtype Posterior Probability
02_AG 0.00000000100965
03_AB 1.2391e-25
04_cpx 0.000000000038611
06_cpx 2.67998e-31
09_cpx 0.00000335348
11_cpx 2.85857e-20
13_cpx 9.95928e-29
16_A2D 0.000568462
A 0.0115902
H 0.987838
K 0.0000000000000013044

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 131 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  H  K
   02_AG     35     0      0      0      0      0      0      0  0  0  0
   03_AB      0     0      0      0      0      0      0      0  0  0  0
   04_cpx     0     0      1      0      0      0      0      0  2  0  0
   06_cpx     0     0      0      6      0      0      0      0  0  0  0
   09_cpx     0     0      0      0      3      0      0      0  1  0  0
   11_cpx     0     0      0      1      0      8      0      0  0  0  0
   13_cpx     0     0      0      0      0      0      3      0  0  0  0
   16_A2D     0     0      0      0      0      0      0      2  0  0  0
   A          0     1      3      0      0      0      0      2 57  0  0
   H          0     0      0      0      0      0      0      0  0  3  0
   K          0     0      0      0      0      1      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