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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 0 232 169 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60074 CAA77496 gag 0 77 61 B B B (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 0.623946 (all), 0.589716 (group)
Subtype Posterior Probability
01_AE 0.00000000000000928289
A 0.00000000000568621
B 1
C 0.000000000000167688
D 0.0000000227742
F 0.00000000000312093
G 1.94414e-17
H 0.00000000004559
J 0.0000000917426
K 0.0000000000129296

Cross-Validation of Discriminant Models
Miss-Classification Rate: 28 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   2   0   0   0   0   0   0   0
    A         3 127   0   0   2   0   1   0   0
    B         0   1 261   0   2   1   0   0   0
    C         0   0   0 553   0   0   0   0   0
    D         0   0   2   0  73   0   1   0   0
    F         0   0   0   0   0  10   0   3   2
    G         0   0   0   0   0   0  20   1   0
    H         0   0   0   0   1   2   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   2   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.661192 (all), 0.677576 (group)
Subtype Posterior Probability
03_AB 0.0000000000000520028
07_BC 0.0000000000180468
08_BC 2.68281e-19
12_BF 0.0000000000133732
14_BG 8.26458e-18
15_01B 5.85076e-20
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      3     0     0      0   0
   08_BC      0     5     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     1      0 264

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