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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
env 0 336 212 J 11_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
87246733 ABD35433 env 0 112 77 A 02_AG Undecided


Detailed result for env (major) Outlierness: 0.513255 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0000000000000160838
A 0.0000530561
B 0.00000600383
C 0.0000145893
D 0.0000000155017
F 0.000027665
G 0.000000294799
H 0.000227311
J 0.998085
K 0.00158593

Cross-Validation of Discriminant Models
Miss-Classification Rate: 9 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   0   0   0   0   0   0   0   0   0
    A         0  81   0   0   0   0   0   0   0   1
    B         0   0 454   0   0   0   0   0   0   0
    C         0   0   0 463   0   0   0   0   1   0
    D         0   0   0   0  57   0   0   2   1   0
    F         0   0   0   0   0  16   0   0   0   0
    G         0   0   0   0   0   0  23   0   0   0
    H         0   0   0   0   0   0   0   2   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 3.06511 (all), 4.46064 (group)
Subtype Posterior Probability
06_cpx 0
11_cpx 0.999432
13_cpx 1.79289e-35
J 0.000568205

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 21 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      6      0      0
   11_cpx      0     11      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