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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
37693964 AAP33765 tat 0 88 79 A A A (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 2.84469 (all), 40.655 (group)
Subtype Posterior Probability
01_AE 0.00000000384235
A 0.0462676
B 4.86509e-16
C 0.00000140808
D 0.0000000000000100045
F 5.47504e-27
G 0.00000000866006
H 0.354121
J 0.0261481
K 0.573462

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 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  51   1   1   0   1   1   0   0   2
    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: 5.35799 (all), 26.003 (group)
Subtype Posterior Probability
02_AG 0.000176002
03_AB 0.000000000511658
04_cpx 0.0000187164
06_cpx 2.71539e-27
09_cpx 0.0000000059835
11_cpx 1.54281e-24
13_cpx 1.79826e-32
16_A2D 0.702275
A 0.297521
H 0.00000941312
J 0.00000000000200217
K 1.38357e-21

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 132 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  H  J  K
   02_AG     35     0      0      0      0      0      0      0  0  0  0  0
   03_AB      0     0      0      0      0      0      0      0  0  0  0  0
   04_cpx     0     0      0      0      0      0      0      0  3  0  0  0
   06_cpx     0     0      0      6      0      0      0      0  0  0  0  0
   09_cpx     0     0      0      0      3      0      0      0  1  0  0  0
   11_cpx     0     0      0      0      0      8      0      0  0  0  0  1
   13_cpx     0     0      0      0      0      0      3      0  0  0  0  0
   16_A2D     0     0      0      0      0      0      0      2  0  0  0  0
   A          0     1      2      0      0      0      0      1 58  1  0  0
   H          0     0      0      0      0      0      0      0  0  3  0  0
   J          0     0      0      0      0      0      0      0  0  0  0  0
   K          0     0      0      0      0      0      0      0  0  0  1  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