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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 0 629 571 K 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134145542 ABO63028 pol 0 209 195 J 05_DF Undecided


Detailed result for pol (major) Outlierness: 1.02525 (all), 13.626 (group)
Subtype Posterior Probability
01_AE 0.00000000000000151284
A 1.95932e-21
B 0.00000974261
C 3.52953e-31
D 6.07539e-19
F 0.00000517546
G 3.10383e-27
H 0.0000000000714476
J 0.000000000000722385
K 0.999985

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: 2.0412 (all), 15.6596 (group)
Subtype Posterior Probability
04_cpx 1
06_cpx 0.000000136076
K 2.24463e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 9 / 10 at 9 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      0      0 3
   06_cpx      1      1 3
   K           0      2 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