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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
5tat 0 144 124 K 16_A2D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693978 AAP33772 tat 0 86 79 A A A (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 2.69333 (all), 12.1811 (group)
Subtype Posterior Probability
01_AE 0.00000000000697746
A 0.0257861
B 7.38765e-21
C 0.000000481682
D 1.41781e-17
F 1.35721e-35
G 0.000000128786
H 0.000321422
J 0.00000000689162
K 0.973892

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    50   0   0   0   0   0   3   0   0   0
    A         7  51   1   1   0   0   1   0   0   2
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   0  11   0   1   0   0
    G         2   0   0   0   0   0  13   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 4.19616 (all), 19.7771 (group)
Subtype Posterior Probability
02_AG 0.00000000000155957
03_AB 3.47802e-31
04_cpx 9.33018e-18
06_cpx 2.49206e-30
09_cpx 0.0000186593
11_cpx 5.16013e-22
13_cpx 0
16_A2D 0.999981
A 0.0000000239634
K 1.71469e-20

Cross-Validation of Discriminant Models
Miss-Classification Rate: 14 / 128 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  K
   02_AG     35     0      0      0      0      0      0      0  0  0
   03_AB      0     0      0      0      0      0      0      0  0  0
   04_cpx     0     0      0      0      0      0      0      0  3  0
   06_cpx     0     0      0      6      0      0      0      0  0  0
   09_cpx     0     0      0      0      2      0      0      0  2  0
   11_cpx     0     0      0      0      0      8      0      0  0  1
   13_cpx     0     0      0      0      0      0      3      0  0  0
   16_A2D     0     0      0      0      0      0      0      2  0  0
   A          0     1      3      0      0      0      0      2 57  0
   K          0     0      0      1      0      0      0      0  0  1

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