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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 3 554 496 K B Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
71392182 AAZ31962 pol 0 184 171 C C C (Unambiguous Nested)


Detailed result for pol (major) Outlierness: 0.450299 (all), 13.6701 (group)
Subtype Posterior Probability
01_AE 3.17453e-20
A 1.0509e-16
B 0.017882
C 0.00000556326
D 0.000000383225
F 0.00000000148741
G 0.000000000012147
H 0.0774878
J 0.000108375
K 0.904516

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 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         3  55   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   1   0  45   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: 1.05086 (all), 2.32738 (group)
Subtype Posterior Probability
03_AB 0.180133
04_cpx 0
06_cpx 2.73336e-23
07_BC 0.128242
08_BC 0.000039929
12_BF 0.000000000000942489
14_BG 1.03435e-36
15_01B 1.0609e-36
B 0.691585
H 1.60143e-19
K 9.95078e-16

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 197 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 12_BF 15_01B   B   H   K
   03_AB       0      0     0      0   0   0   0
   04_cpx      3      0     0      0   0   0   0
   06_cpx      0      5     0      0   0   0   0
   07_BC       0      0     0      0   0   0   0
   08_BC       0      0     0      0   0   0   0
   12_BF       0      0     7      0   2   0   0
   14_BG       0      0     0      0   0   0   0
   15_01B      0      0     0      3   0   0   0
   B           0      0     2      0 166   0   0
   H           0      0     0      0   0   3   0
   K           0      0     0      0   0   0   2

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