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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
gag 0 182 128 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60098 CAA77490 gag 0 60 46 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.629188 (all), 0.571848 (group)
Subtype Posterior Probability
01_AE 0.00000000000279915
A 0.0000000146694
B 0.999851
C 0.00000000639277
D 0.0000000355151
F 0.0000000185072
G 0.000000000141069
H 0.000000207327
J 0.000148353
K 0.000000063039

Cross-Validation of Discriminant Models
Miss-Classification Rate: 33 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    67   4   0   0   1   0   0   0   0   0
    A         2 128   0   0   2   0   1   0   0   0
    B         0   1 260   0   3   0   0   0   1   0
    C         0   0   0 551   0   0   2   0   0   0
    D         0   2   1   0  73   0   0   0   0   0
    F         0   0   1   0   1  10   2   1   0   0
    G         0   0   0   0   1   1  19   0   0   0
    H         0   0   0   0   0   1   0   1   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         1   1   1   0   0   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.683715 (all), 0.6519 (group)
Subtype Posterior Probability
03_AB 0.00000000289589
07_BC 0.0000000000000171247
08_BC 0.00000000000000985981
12_BF 0.000000000184476
14_BG 3.70686e-16
15_01B 3.44521e-18
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 290 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      0     2     1     0      0   0
   08_BC      0     0     5     0      0   0
   12_BF      0     0     0     8      0   2
   14_BG      0     0     0     0      0   0
   15_01B     0     0     0     0      5   0
   B          1     0     0     1      0 263

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