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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 0 666 565 K 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
110734836 ABG88988 pol 0 222 193 G 02_AG Undecided


Detailed result for pol (major) Outlierness: 0.755582 (all), 145.801 (group)
Subtype Posterior Probability
01_AE 1.24014e-19
A 0.0000000164112
B 0.00000000117528
C 3.86815e-23
D 0.00000000000199819
F 0.00000215299
G 0.000456791
H 0.000276124
J 0.000175511
K 0.999089

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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         1  57   0   1   0   0   0   0   0
    B         0   0 167   0   0   1   0   0   0
    C         0   0   0 370   0   0   0   1   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   2   1
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 8.87077 (all), 7.14909 (group)
Subtype Posterior Probability
04_cpx 1
06_cpx 1.18936e-26
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 10 at 8 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      1      1 1
   06_cpx      0      4 1
   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