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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
37693860 AAP33713 tat 0 86 79 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 3.84814 (all), 13.4881 (group)
Subtype Posterior Probability
01_AE 0.0000551744
A 0.0000000000757177
B 0.00000000138107
C 8.23782e-22
D 8.85418e-30
F 2.7474e-31
G 0.999945
H 0.0000000000000260193
J 0.00000000000000125334
K 2.56219e-21

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    52   0   0   0   0   0   1   0   0   0
    A         7  51   1   0   0   1   1   1   0   1
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 306   0   0   0   1   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: 5.59394 (all), 66.7256 (group)
Subtype Posterior Probability
02_AG 0.0000000161145
04_cpx 2.25012e-17
06_cpx 0
09_cpx 1.05097e-42
11_cpx 0
13_cpx 0
14_BG 1
G 0.000000000000266301

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      2      0      0      0      0     0  1
   06_cpx     0      0      6      0      0      0     0  0
   09_cpx     0      0      0      4      0      0     0  0
   11_cpx     0      0      1      0      8      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