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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 0 708 649 J 11_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
58978995 AAW83282 pol 0 235 221 D D D (Major agrees Nested with high confidence)


Detailed result for pol (major) Outlierness: 0.894515 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 1.43582e-28
A 1.35287e-20
B 0.00000115767
C 0.000000000000335231
D 0.00000000112575
F 1.86118e-29
G 0.00000000000239857
H 0.00860052
J 0.991398
K 0.000000354478

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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         2  56   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   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   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: 2.79113 (all), 14.0054 (group)
Subtype Posterior Probability
06_cpx 5.66485e-30
11_cpx 1
13_cpx 0
J 0

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