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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
pol 0 589 534 F K Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134146021 ABO63267 pol 0 196 183 A 04_cpx Undecided


Detailed result for pol (major) Outlierness: 1.2355 (all), 10.7356 (group)
Subtype Posterior Probability
01_AE 0.00000000000174985
A 2.46814e-19
B 0.000505804
C 8.01622e-26
D 0.0000000000149727
F 0.795719
G 0.000000000801714
H 5.51085e-18
J 0.0000000108688
K 0.203776

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         3  55   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         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 pol (nested) Outlierness: 4.06469 (all), 17.7291 (group)
Subtype Posterior Probability
04_cpx 0
05_DF 1.32191e-38
06_cpx 1.63826e-41
12_BF 6.13769e-43
F 9.05759e-31
K 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 0 / 34 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 05_DF 06_cpx 12_BF  F  K
   04_cpx      3     0      0     0  0  0
   05_DF       0     3      0     0  0  0
   06_cpx      0     0      5     0  0  0
   12_BF       0     0      0     9  0  0
   F           0     0      0     0 12  0
   K           0     0      0     0  0  2

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