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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 0 300 234 K 02_AG Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
121073588 ABM47199 pol 0 100 80 01_AE 09_cpx Undecided


Detailed result for pol (major) Outlierness: 1.06318 (all), 275.651 (group)
Subtype Posterior Probability
01_AE 0.351114
A 0.0578797
B 0.00000000000000129803
C 0.00000150813
D 0.00000000197856
F 0.000000000000162636
G 0.0278269
H 0.00568367
J 0.0384788
K 0.519016

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 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         6  53   0   0   0   0   0   0   0   0
    B         0   0 162   0   3   3   0   0   0   0
    C         0   0   0 370   0   0   0   0   0   1
    D         0   3   0   0  43   0   0   0   0   0
    F         0   1   0   0   1  10   0   0   0   0
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   0   0   0   1   1   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 1.64419 (all), 3.99272 (group)
Subtype Posterior Probability
01_AE 0.00000000000865457
02_AG 0.979235
03_AB 0.000000000000909464
04_cpx 0.00000163759
06_cpx 0.0000303208
09_cpx 0.013294
11_cpx 0
13_cpx 1.82859e-31
14_BG 0.0000000000020141
15_01B 2.70735e-18
16_A2D 5.09992e-18
A 0.0000000171637
G 0.000000089381
J 6.75702e-37
K 0.00743945

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 210 at 10 Dimensional MDS
         Predicted
Objective 01_AE 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG 15_01B 16_A2D  A
   01_AE     55     0      0      0      0      0      0     0      2      0  0
   02_AG      0    42      0      1      0      0      0     0      0      0  0
   03_AB      0     0      0      0      0      0      0     0      0      0  0
   04_cpx     0     0      2      0      0      0      0     0      0      0  1
   06_cpx     0     0      0      4      0      0      0     0      0      0  0
   09_cpx     0     0      0      0      4      0      0     0      0      0  0
   11_cpx     0     0      0      0      0     10      0     0      0      0  0
   13_cpx     0     0      0      0      0      0      3     0      0      0  0
   14_BG      0     0      0      0      0      0      0     0      0      0  0
   15_01B     3     0      0      0      0      0      0     0      0      0  0
   16_A2D     1     0      0      0      0      0      0     0      0      1  0
   A          2     1      0      0      1      0      0     0      0      0 55
   G          0     0      0      3      0      0      0     1      0      0  0
   J          0     0      0      0      0      0      0     0      0      0  0
   K          0     0      0      0      2      0      0     0      0      0  0
         Predicted
Objective  G
   01_AE   0
   02_AG   0
   03_AB   0
   04_cpx  0
   06_cpx  1
   09_cpx  0
   11_cpx  0
   13_cpx  0
   14_BG   0
   15_01B  0
   16_A2D  0
   A       0
   G      12
   J       0
   K       0

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