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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 0 666 565 K 06_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
110734852 ABG88996 pol 0 222 193 G 02_AG Undecided


Detailed result for pol (major) Outlierness: 0.767651 (all), 13.4236 (group)
Subtype Posterior Probability
01_AE 8.26419e-19
A 0.000693744
B 0.00000000078033
C 3.89239e-20
D 0.0000000000272234
F 0.00000000000274385
G 0.062685
H 0.0000123858
J 0.0122302
K 0.924379

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   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         1  57   0   1   0   0   0   0   0
    B         0   0 167   0   0   1   0   0   0
    C         0   0   0 370   0   0   0   1   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   2   1
    J         0   0   0   0   0   0   0   0   0
    K         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: 0.689223 (all), 2.64515 (group)
Subtype Posterior Probability
02_AG 0.000107877
04_cpx 0
06_cpx 0.999887
09_cpx 2.88321e-26
11_cpx 0
13_cpx 0
14_BG 0.000000000108747
G 0.00000505375
J 2.8026e-45
K 1.27625e-16

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 88 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G  K
   02_AG     43      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     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
   G          0      0      0      0      0      0     2 14  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


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea