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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
9629357 NC_001802 5tat 5376 5587 185 B B B (Unambiguous Nested)
env 5770 8341 1585 B B B (Unambiguous Nested)
gag 335 1838 963 B B B (Unambiguous Nested)
ltr 8631 9181 256 B B B (Unambiguous Nested)
nef 8342 8963 246 B B B (Unambiguous Nested)
pol 1630 4642 2703 B B B (Unambiguous Nested)
vif 4586 5165 522 B B B (Unambiguous Nested)
vpr 5104 5396 147 B B B (Unambiguous Nested)
vpu 5620 5856 95 B B B (Major agrees Nested with high confidence)


Detailed result for tat (major) Outlierness: 0.89282 (all), 0.735298 (group)
Subtype Posterior Probability
01_AE 3.53893e-32
A 1.00152e-22
B 1
C 1.20696e-23
D 3.32744e-11
F 1.44537e-12
G 6.79208e-24
H 6.50357e-25
J 9.71249e-20
K 2.11437e-21

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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         0  61   0   0   0   0   0   0   2   0
    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   1   1  10   0   0   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   0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for tat (nested) Outlierness: 0.651976 (all), 0.610007 (group)
Subtype Posterior Probability
03_AB 4.47129e-05
07_BC 7.28785e-40
08_BC 0
12_BF 4.16767e-11
14_BG 0
15_01B 0
B 0.999955

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 176 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      7     0      0   3
   14_BG      0     2      0   0
   15_01B     0     1      1   0
   B          0     0      0 159

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