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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
ltr 310 378 54 ? B B Undecided


Detailed result for ltr (major) Outlierness: 4.18186 (all), 11.6338 (group)
Subtype Posterior Probability
01_AE 2.15875e-39
A 6.26526e-16
B 0.999998
C 7.26212e-38
D 1.47168e-27
F 0.000002438
G 8.22629e-33
H 7.00649e-45
J 4.32781e-23
K 0.0000000000011271

Cross-Validation of Discriminant Models
Miss-Classification Rate: 23 / 276 at 10 Dimensional MDS
         Predicted
Objective 01_AE  A  B  C  D  F  G  H  J  K
    01_AE    52  0  0  0  0  0  0  0  0  0
    A         0 18  4  0  1  1  0  0  0  1
    B         1  0 60  0  0  1  0  0  0  0
    C         0  2  0 72  0  0  0  1  0  0
    D         0  0  3  0 35  0  0  0  0  0
    F         0  3  1  0  0  4  0  0  0  0
    G         0  0  0  0  0  0  8  1  0  0
    H         2  1  0  0  0  0  0  0  0  0
    J         0  0  0  0  0  0  0  0  2  0
    K         0  0  0  0  0  0  0  0  0  2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (nested) Outlierness: 8.57507 (all), 11.3066 (group)
Subtype Posterior Probability
03_AB 1.14458e-23
07_BC 0
08_BC 0
12_BF 4.86526e-32
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 74 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF  B
    03_AB     2     0     0     0  0
    07_BC     0     0     2     0  0
    08_BC     0     0     5     0  0
    12_BF     1     0     0     1  1
    B         0     1     1     1 59

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