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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 0 196 143 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60065 CAA44008 gag 0 64 51 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.642283 (all), 0.495039 (group)
Subtype Posterior Probability
01_AE 0.00000000000000512788
A 0.000000000983621
B 0.999976
C 0.0000000000342201
D 0.00000872877
F 0.000000155609
G 5.61445e-17
H 0.000000000169472
J 0.0000151461
K 0.0000000000468705

Cross-Validation of Discriminant Models
Miss-Classification Rate: 27 / 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         0 130   0   0   2   0   1   0   0   0
    B         0   1 260   1   2   0   0   0   1   0
    C         0   1   0 551   0   0   0   1   0   0
    D         0   2   2   1  71   0   0   0   0   0
    F         0   0   0   1   0  14   0   0   0   0
    G         0   0   0   0   1   0  20   0   0   0
    H         0   0   0   0   0   2   0   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.607013 (all), 0.567809 (group)
Subtype Posterior Probability
03_AB 0.00000000000107339
07_BC 0.0000000000000210795
08_BC 0.00000000000000548232
12_BF 0.00000122101
14_BG 2.51834e-18
15_01B 1.73699e-21
B 0.999999

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