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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 0 630 572 K 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134147071 ABO63790 pol 0 210 196 F F Undecided


Detailed result for pol (major) Outlierness: 0.725874 (all), 23.3981 (group)
Subtype Posterior Probability
01_AE 0.000000000000976941
A 0.00000000955834
B 2.55303e-16
C 2.95385e-16
D 1.31623e-25
F 0.00430003
G 2.12172e-30
H 0.00891122
J 5.60407e-20
K 0.986789

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 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         2  56   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: 1.59484 (all), 6.54133 (group)
Subtype Posterior Probability
04_cpx 1
06_cpx 5.24444e-17
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 10 at 8 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      1      0 2
   06_cpx      0      3 2
   K           1      1 0

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