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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 0 616 561 J B Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
10944865 CAC14102 pol 0 205 192 B H Undecided


Detailed result for pol (major) Outlierness: 1.08877 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 3.92921e-37
A 1.2331e-28
B 0.0579794
C 0.0000000000119502
D 0.0000000000162985
F 1.55222e-27
G 0.00000000000363223
H 0.0000324183
J 0.941985
K 0.00000335999

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         2  56   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   0
    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: 1.85139 (all), 4.05472 (group)
Subtype Posterior Probability
03_AB 0.000000581996
06_cpx 3.71222e-29
07_BC 0.00000964844
08_BC 0.000000000140556
11_cpx 0
12_BF 8.56512e-18
13_cpx 0
14_BG 0.000000000000878619
15_01B 0
B 0.99999
J 1.08001e-30

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 203 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 12_BF 13_cpx 15_01B   B
   03_AB       0      0     0      0      0   0
   06_cpx      5      0     0      0      0   0
   07_BC       0      0     0      0      0   0
   08_BC       0      0     0      0      0   0
   11_cpx      0     10     0      0      0   0
   12_BF       0      0     7      0      0   2
   13_cpx      0      0     0      3      0   0
   14_BG       0      0     0      0      0   0
   15_01B      0      0     0      0      3   0
   B           0      0     1      0      0 167
   J           0      0     0      0      0   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