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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 0 207 156 A A A (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60080 CAA77500 gag 0 66 53 01_AE A Undecided


Detailed result for gag (major) Outlierness: 0.807205 (all), 0.893803 (group)
Subtype Posterior Probability
01_AE 0.0000217069
A 0.999978
B 1.89463e-16
C 6.7079e-16
D 0.000000000000253716
F 3.66225e-16
G 0.000000000121878
H 0.0000000000000144491
J 0.0000000000000142104
K 0.00000000658152

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   2   0   0   0   0   0   0   0   0
    A         1 129   0   0   2   0   1   0   0   0
    B         0   1 262   0   1   1   0   0   0   0
    C         0   1   0 551   0   0   1   0   0   0
    D         0   2   1   0  72   0   1   0   0   0
    F         0   0   0   0   1  14   0   0   0   0
    G         0   0   0   0   0   0  21   0   0   0
    H         0   0   0   0   0   2   0   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.66906 (all), 0.656017 (group)
Subtype Posterior Probability
02_AG 0.000000000414452
03_AB 0.000394597
04_cpx 0.000000171074
06_cpx 0.000000315985
09_cpx 0.00012042
11_cpx 0.000000856381
13_cpx 0.0000000282139
16_A2D 0.00000000151579
A 0.999484

Cross-Validation of Discriminant Models
Miss-Classification Rate: 25 / 225 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D   A
   02_AG     57     0      0      0      0      1      0      0   1
   03_AB      0     0      0      0      0      0      0      0   0
   04_cpx     0     0      1      2      0      0      0      0   0
   06_cpx     0     0      3      5      0      0      1      0   0
   09_cpx     0     0      0      0      0      0      0      0   5
   11_cpx     0     0      0      0      0      9      0      0   1
   13_cpx     0     0      1      0      0      0      2      0   0
   16_A2D     0     0      0      0      1      0      0      1   0
   A          0     2      0      0      2      1      1      2 125

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