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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 0 660 602 B B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
3930638 AAC80486 pol 0 220 206 B B B (Unambiguous Nested)


Detailed result for pol (major) Outlierness: 0.612882 (all), 1.25458 (group)
Subtype Posterior Probability
01_AE 2.11582e-41
A 8.40933e-40
B 1
C 1.15717e-36
D 0.0000000000044044
F 1.10347e-33
G 3.11241e-29
H 1.03292e-23
J 2.23494e-16
K 2.26566e-17

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: 0.549652 (all), 1.32586 (group)
Subtype Posterior Probability
03_AB 0.000000147634
07_BC 5.46368e-39
08_BC 1.61959e-27
12_BF 0.0000000000000985959
14_BG 1.4013e-45
15_01B 0
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 184 at 10 Dimensional MDS
         Predicted
Objective 12_BF 15_01B   B
   03_AB      0      0   0
   07_BC      0      0   0
   08_BC      0      0   0
   12_BF      7      0   2
   14_BG      0      0   0
   15_01B     0      3   0
   B          2      0 166

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