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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 K 16_A2D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693962 AAP33764 tat 0 86 79 D D D (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 3.18522 (all), 19.8796 (group)
Subtype Posterior Probability
01_AE 0.00000152713
A 0.316598
B 2.11218e-21
C 0.0000000157096
D 9.51164e-16
F 2.21861e-27
G 0.000000000951061
H 0.0126523
J 0.00188413
K 0.668864

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    51   0   0   0   0   0   2   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: 5.01442 (all), 21.6 (group)
Subtype Posterior Probability
02_AG 0.00000000139978
03_AB 1.346e-17
04_cpx 0.0000000135087
06_cpx 2.34569e-23
09_cpx 0.00357083
11_cpx 1.16451e-25
13_cpx 1.07398e-35
16_A2D 0.929153
A 0.0672753
H 0.000000721211
K 1.29655e-25

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 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      0      0      0      0      0      0  3  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      0      0      8      0      0  0  0  1
   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      2      0      0      0      0      1 57  2  0
   H          0     0      0      0      0      0      0      0  0  3  0
   K          0     0      0      1      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