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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 H H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116274041 ABJ92351 pol 0 96 76 H 05_DF Undecided


Detailed result for pol (major) Outlierness: 1.82397 (all), 20.4584 (group)
Subtype Posterior Probability
01_AE 0.00000000183073
A 0.000000426805
B 0.00000000131007
C 3.49421e-25
D 0.000680803
F 0.000000000000526576
G 0.00000000000106279
H 0.999307
J 0.00000000743609
K 0.0000120445

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 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         5  53   0   0   0   0   1   0   0
    B         0   0 158   0   6   4   0   0   0
    C         0   0   0 370   0   1   0   0   0
    D         0   3   0   0  43   0   0   0   0
    F         0   0   0   0   1  11   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: 80.0975 (all), 13.0895 (group)
Subtype Posterior Probability
04_cpx 0.00000000000000292317
H 1

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

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