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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 0 288 222 J 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116273097 ABJ91881 pol 0 96 76 G B Undecided


Detailed result for pol (major) Outlierness: 1.63581 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 3.96043e-18
A 0.000000000145822
B 0.000590461
C 6.01448e-27
D 0.0000000102575
F 1.53738e-16
G 7.0166e-19
H 2.20711e-17
J 0.99941
K 0.0000000000000106052

Cross-Validation of Discriminant Models
Miss-Classification Rate: 27 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    57   0   0   0   0   0   0   0   0   0
    A         7  51   0   0   0   0   1   0   0   0
    B         0   0 158   0   6   3   0   0   1   0
    C         0   0   0 370   0   0   0   0   0   1
    D         0   5   0   0  41   0   0   0   0   0
    F         0   0   0   0   1  11   0   0   0   0
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 3.70676 (all), 5.58162 (group)
Subtype Posterior Probability
06_cpx 0.999998
11_cpx 0
13_cpx 0
J 0.0000016352

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 19 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      5      0      0
   11_cpx      0     10      0
   13_cpx      0      0      3
   J           0      0      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