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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
gag 0 265 243 ? J 11_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37720744 AAN02246 gag 0 88 83 01_AE 06_cpx Undecided


Detailed result for gag (major) Outlierness: 1.11674 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.336876
A 0.0000741135
B 0.0000000017736
C 2.48059e-17
D 0.00000198675
F 1.4346e-19
G 0.000000000637208
H 0.0000150158
J 0.663033
K 8.03759e-20

Cross-Validation of Discriminant Models
Miss-Classification Rate: 19 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    69   2   1   0   0   0   0   0   0
    A         2 128   0   1   0   0   1   1   0
    B         0   0 261   0   2   2   0   0   0
    C         0   0   0 552   1   0   0   0   0
    D         0   0   1   0  74   0   1   0   0
    F         0   0   0   0   0  14   0   0   1
    G         0   0   0   0   0   0  21   0   0
    H         0   0   0   0   1   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   1   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 2.55419 (all), 4.76333 (group)
Subtype Posterior Probability
01_AE 0.281207
06_cpx 0.00882527
11_cpx 0.70876
13_cpx 3.08286e-44
15_01B 0.0012075
J 0.00000000403963

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 100 at 10 Dimensional MDS
         Predicted
Objective 01_AE 06_cpx 11_cpx 13_cpx 15_01B
   01_AE     71      0      0      0      1
   06_cpx     0      9      0      0      0
   11_cpx     0      0     10      0      0
   13_cpx     0      0      0      3      0
   15_01B     5      0      0      0      0
   J          0      0      0      0      0

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