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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 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37720756 AAN02252 gag 0 88 83 01_AE 01_AE 01_AE (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 1.36251 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0011535
A 0.000000588604
B 0.000000190798
C 9.3276e-20
D 0.000257184
F 2.64465e-18
G 0.0000000000746449
H 0.0000379567
J 0.998551
K 6.30387e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 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   0   0   3

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 5.58281 (all), 7.52399 (group)
Subtype Posterior Probability
06_cpx 1
11_cpx 3.51743e-26
13_cpx 0
J 0.00000000000134569

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 23 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      9      0      0
   11_cpx      1      9      0
   13_cpx      0      0      3
   J           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