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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 1532 1391 ? K 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
110613614 ABF14418 pol 0 511 474 H 02_AG 02_AG (Unambiguous Nested)


Detailed result for pol (major) Outlierness: 0.796906 (all), 16.2666 (group)
Subtype Posterior Probability
01_AE 3.38432e-22
A 0.00000122548
B 7.00649e-45
C 0
D 0
F 1.2662e-22
G 0.00000000000136673
H 0.0000317506
J 0.0548653
K 0.945102

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 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         0  58   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: 2.87779 (all), 18.9559 (group)
Subtype Posterior Probability
04_cpx 0
06_cpx 1
11_cpx 0
13_cpx 0
J 0
K 1.10579e-27

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 24 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 11_cpx 13_cpx  K
   04_cpx      3      0      0      0  0
   06_cpx      0      5      0      0  0
   11_cpx      0      0     10      0  0
   13_cpx      0      0      0      3  0
   J           0      0      0      0  0
   K           0      0      0      0  2

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