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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 H Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116272846 ABJ91756 pol 0 96 76 B H Undecided


Detailed result for pol (major) Outlierness: 2.36821 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0000000000001946
A 0.000000000000086799
B 0.000113197
C 5.4046e-22
D 0.00109684
F 0.00000000374584
G 0.00000000000000212381
H 0.410456
J 0.588323
K 0.0000106893

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         6  53   0   0   0   0   0   0   0
    B         0   0 158   0   6   4   0   0   0
    C         0   0   0 370   0   0   0   0   1
    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: 3.75499 (all), 12.8987 (group)
Subtype Posterior Probability
04_cpx 0
06_cpx 0.00000000000000115207
11_cpx 0
13_cpx 0
H 1
J 3.64e-40

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 25 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 11_cpx 13_cpx  H
   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
   H           0      0      0      0  3
   J           0      0      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