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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
37693890 AAP33728 tat 0 86 79 B B B (Major agrees Nested with high confidence)


Detailed result for 5tat (major) Outlierness: 4.46268 (all), 17.5148 (group)
Subtype Posterior Probability
01_AE 0.00000000135094
A 0.00000000000026344
B 0.0000000000941232
C 9.74882e-17
D 7.89718e-26
F 7.30768e-29
G 1
H 5.02396e-19
J 8.60361e-21
K 1.14578e-24

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         7  52   1   0   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: 6.97437 (all), 184.301 (group)
Subtype Posterior Probability
02_AG 0.168609
04_cpx 4.91248e-18
06_cpx 0
09_cpx 2.82603e-30
11_cpx 0
13_cpx 4.76465e-32
14_BG 0.831391
G 0.00000018313

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 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     1  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      1      0      8      0     0  0
   13_cpx     0      0      0      0      0      3     0  0
   14_BG      0      0      0      0      0      0     1  1
   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