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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 96 76 G B Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
116273096 DQ876227 pol 0 288 222 J 06_cpx Undecided


Detailed result for pol (major) Outlierness: 2.46273 (all), 3.53641 (group)
Subtype Posterior Probability
01_AE 0.0000175399
A 0.0000535492
B 0.0255453
C 0.0000000113027
D 0.000000217514
F 0.000000000919916
G 0.920612
H 0.0537673
J 0.00000340739
K 0.000000680419

Cross-Validation of Discriminant Models
Miss-Classification Rate: 79 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    49   6   0   1   0   0   0   1   0
    A        14  42   0   1   0   0   1   1   0
    B         0   0 152   1  10   3   0   0   2
    C         1   0   3 364   0   0   1   2   0
    D         4   0   7   0  33   2   0   0   0
    F         2   0   1   1   0   6   0   0   2
    G         3   6   0   0   0   0   6   1   0
    H         1   0   0   0   0   0   0   2   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: 2.75395 (all), 3.37943 (group)
Subtype Posterior Probability
02_AG 0.00932536
03_AB 0.00000923539
04_cpx 0.000000000000127726
06_cpx 0.00007918
07_BC 0.00000000000074192
08_BC 1.31971e-23
09_cpx 0.415776
11_cpx 1.31334e-32
12_BF 0.000000000000015243
13_cpx 7.08461e-31
14_BG 0.0000000594135
15_01B 0.0000000000000167149
B 0.574809
G 0.00000170251
H 0.0000000000000456479

Cross-Validation of Discriminant Models
Miss-Classification Rate: 31 / 271 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 07_BC 09_cpx 11_cpx 12_BF 13_cpx 15_01B   B   G
   02_AG     41      0      1     0      0      0     0      0      0   0   1
   03_AB      0      0      0     0      0      0     0      0      0   0   0
   04_cpx     1      1      0     0      0      0     0      0      1   0   0
   06_cpx     4      0      0     0      0      0     0      0      0   0   1
   07_BC      0      0      0     0      0      0     0      0      0   0   0
   08_BC      0      0      0     0      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
   12_BF      0      0      0     0      0      0     8      0      1   0   0
   13_cpx     0      0      0     0      0      0     0      3      0   0   0
   14_BG      0      0      0     0      0      0     0      0      0   0   0
   15_01B     1      0      0     1      0      0     1      0      0   0   0
   B          0      0      0     0      1      0     3      0      0 164   0
   G          9      0      1     0      0      0     0      0      0   0   6
   H          0      0      0     0      0      0     0      0      0   0   0
         Predicted
Objective   H
   02_AG    0
   03_AB    0
   04_cpx   0
   06_cpx   0
   07_BC    0
   08_BC    0
   09_cpx   0
   11_cpx   0
   12_BF    0
   13_cpx   0
   14_BG    0
   15_01B   0
   B        0
   G        0
   H        3

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