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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 G 14_BG Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693870 AAP33718 tat 0 86 79 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 3.522 (all), 13.8041 (group)
Subtype Posterior Probability
01_AE 0.0000000000140592
A 0.0000000568254
B 0.00558547
C 2.52817e-16
D 7.76342e-18
F 0.00000000000374239
G 0.994414
H 0.000000577755
J 0.000000000000321867
K 2.85721e-18

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    52   0   0   0   0   0   1   0   0   0
    A         7  51   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: 6.36568 (all), 61.196 (group)
Subtype Posterior Probability
02_AG 7.55918e-16
04_cpx 7.56196e-28
06_cpx 2.29863e-32
09_cpx 1.49799e-42
11_cpx 0
13_cpx 1.64298e-24
14_BG 1
G 0.00000000000146071

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 77 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G
   02_AG     35      0      0      0      0      0     0  0
   04_cpx     0      3      0      0      0      0     0  0
   06_cpx     0      0      6      0      0      0     0  0
   09_cpx     0      0      0      4      0      0     0  0
   11_cpx     0      0      2      0      7      0     0  0
   13_cpx     0      0      0      0      0      3     0  0
   14_BG      0      0      0      0      0      0     2  0
   G          0      0      0      0      0      0     1 14

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