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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 0 573 518 ? H 16_A2D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
45645049 AAS73188 pol 0 191 178 D H Undecided


Detailed result for pol (major) Outlierness: 1.27887 (all), 31.1731 (group)
Subtype Posterior Probability
01_AE 0.00000000449207
A 0.168134
B 0.000000000000011576
C 2.72172e-17
D 4.33656e-29
F 1.28863e-41
G 1.11736e-19
H 0.831866
J 0.0000000304594
K 2.2629e-17

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    57   0   0   0   0   0   0   0   0   0
    A         3  55   0   1   0   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0   0
    C         0   0   0 370   0   0   0   1   0   0
    D         0   0   0   0  46   0   0   0   0   0
    F         0   0   0   0   0  12   0   0   0   0
    G         0   0   0   0   0   0  16   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   0   0   0   0   0   0   0   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 2.60348 (all), 30.3539 (group)
Subtype Posterior Probability
02_AG 1.21913e-43
03_AB 0.000000000000128782
04_cpx 0
06_cpx 7.24973e-28
09_cpx 4.11994e-33
11_cpx 7.42952e-18
13_cpx 3.95004e-17
16_A2D 1
A 0.000000000379963
H 7.70894e-25

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 133 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  H
   02_AG     43      0      0      0      0      0      0  0  0
   03_AB      0      0      0      0      0      0      0  0  0
   04_cpx     0      3      0      0      0      0      0  0  0
   06_cpx     0      0      5      0      0      0      0  0  0
   09_cpx     0      0      0      4      0      0      0  0  0
   11_cpx     0      0      0      0      9      1      0  0  0
   13_cpx     0      0      0      0      2      1      0  0  0
   16_A2D     0      0      0      0      0      0      2  0  0
   A          0      0      0      0      0      0      2 56  1
   H          0      0      0      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