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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 0 231 167 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
939875 CAA77497 gag 0 76 60 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.788205 (all), 0.730609 (group)
Subtype Posterior Probability
01_AE 0.0000000000000704267
A 0.00000000000066647
B 0.999912
C 0.0000000000000230967
D 0.00000000246043
F 0.00000000000423974
G 3.84011e-17
H 0.0000000000266585
J 0.0000880627
K 0.000000000761565

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   2   0   0   0   0   0   0   0   0
    A         1 128   0   0   2   0   1   0   0   1
    B         0   1 262   0   1   1   0   0   0   0
    C         0   0   0 553   0   0   0   0   0   0
    D         0   1   1   0  74   0   0   0   0   0
    F         0   0   0   0   1  14   0   0   0   0
    G         0   0   0   0   0   0  20   1   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: 0.413887 (all), 0.396727 (group)
Subtype Posterior Probability
03_AB 0.00000000000717447
07_BC 0.00000000000000891684
08_BC 1.83517e-22
12_BF 0.000000000372572
14_BG 1.81673e-22
15_01B 3.35316e-20
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 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      3     0     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     0      0 265

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