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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 H D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693918 AAP33742 tat 0 86 79 A C Undecided


Detailed result for 5tat (major) Outlierness: 2.24323 (all), 56.9726 (group)
Subtype Posterior Probability
01_AE 0.000000000000978042
A 0.00000421963
B 0.0000000013097
C 0.0000000433521
D 0.0188089
F 1.20933e-16
G 0.00000000020145
H 0.981187
J 0.00000000312528
K 0.00000000360873

Cross-Validation of Discriminant Models
Miss-Classification Rate: 19 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    52   0   0   0   0   0   1   0   0   0
    A         6  52   1   1   0   1   1   0   0   1
    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   2   9   0   1   0   0
    G         0   0   0   0   0   0  15   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: 5.41706 (all), 5.41482 (group)
Subtype Posterior Probability
04_cpx 9.51623e-23
05_DF 0.000000144829
10_CD 2.37416e-38
16_A2D 0.00000203725
D 0.999998
H 0.00000000802503

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 57 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 05_DF 10_CD 16_A2D  D  H
   04_cpx      3     0     0      0  0  0
   05_DF       0     0     0      0  3  0
   10_CD       0     0     2      0  0  0
   16_A2D      0     1     0      1  0  0
   D           0     2     0      0 42  0
   H           0     0     0      0  0  3

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