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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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 0 221 192 G 02_AG Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
110734853 DQ682723 pol 1 664 562 K 04_cpx Undecided


Detailed result for pol (major) Outlierness: 0.852704 (all), 2.61737 (group)
Subtype Posterior Probability
01_AE 0.000000602049
A 0.0244841
B 0.000000000791227
C 0.00000401362
D 0.000790623
F 0.0000000624948
G 0.974716
H 0.0000023807
J 0.0000000748087
K 0.00000260008

Cross-Validation of Discriminant Models
Miss-Classification Rate: 42 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    55   2   0   0   0   0   0   0   0
    A         3  48   0   0   0   1   5   2   0
    B         0   0 162   1   2   2   0   0   1
    C         0   1   0 368   0   0   0   2   0
    D         0   0   2   0  41   3   0   0   0
    F         0   0   0   0   1   9   0   0   2
    G         1   6   0   0   0   0   8   1   0
    H         0   1   0   0   0   0   0   0   2
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 1.21295 (all), 1.21354 (group)
Subtype Posterior Probability
02_AG 0.950825
03_AB 0.0000156846
04_cpx 0.0000669787
06_cpx 0.00297688
09_cpx 0.0000429051
11_cpx 2.37126e-32
13_cpx 1.70418e-19
14_BG 0.0027572
16_A2D 0.00000000145645
A 0.0000129717
G 0.0433027

Cross-Validation of Discriminant Models
Miss-Classification Rate: 28 / 147 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  G
   02_AG     34      1      1      2      0      0      0  0  5
   03_AB      0      0      0      0      0      0      0  0  0
   04_cpx     1      1      0      0      0      0      0  1  0
   06_cpx     3      0      0      0      0      0      0  2  0
   09_cpx     0      0      0      4      0      0      0  0  0
   11_cpx     0      0      0      0     10      0      0  0  0
   13_cpx     0      0      0      0      0      3      0  0  0
   14_BG      0      0      0      0      0      0      0  0  0
   16_A2D     0      0      0      0      0      0      2  0  0
   A          0      0      0      0      0      0      2 56  1
   G          4      1      1      1      0      0      0  0  9

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