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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 0 183 129 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60072 CAA77495 gag 0 61 47 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.925807 (all), 0.813562 (group)
Subtype Posterior Probability
01_AE 0.00000000000015311
A 3.86547e-16
B 1
C 9.17139e-17
D 0.0000000000152917
F 0.00000000000000246393
G 1.5231e-21
H 0.00000000000144796
J 0.00000000255831
K 0.0000000000330991

Cross-Validation of Discriminant Models
Miss-Classification Rate: 31 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    68   3   0   0   1   0   0   0   0   0
    A         1 128   0   0   2   0   1   0   0   1
    B         0   1 260   0   3   0   0   0   1   0
    C         0   1   0 551   0   0   1   0   0   0
    D         0   2   1   1  72   0   0   0   0   0
    F         0   0   1   0   1  11   1   1   0   0
    G         0   0   0   0   1   0  20   0   0   0
    H         0   0   0   0   0   1   0   1   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         1   1   1   0   0   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 1.3272 (all), 1.33216 (group)
Subtype Posterior Probability
03_AB 0.00000000595946
07_BC 5.2593e-18
08_BC 5.75744e-17
12_BF 0.0000000000000766585
14_BG 2.54098e-16
15_01B 7.68595e-18
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      2     1     0      0   0
   08_BC      0     5     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     1      0 264

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