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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
gag 0 74 59 B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60091 Z11136 gag 0 225 168 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.996061 (all), 1.02774 (group)
Subtype Posterior Probability
01_AE 0.000188232
A 0.000408051
B 0.975838
C 0.000102309
D 0.0000176673
F 0.0000000174375
G 0.000000502758
H 0.0000605233
J 0.000000473542
K 0.023384

Cross-Validation of Discriminant Models
Miss-Classification Rate: 203 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    37  30   2   1   1   0   1   0   0
    A        12 112   1   6   1   0   1   0   0
    B         3   9 225  11  11   3   0   1   2
    C        10  30  16 487   0   2   8   0   0
    D         3   3  11   3  56   0   0   0   0
    F         0   0   1   1   0  11   2   0   0
    G         3   1   1   4   1   0  11   0   0
    H         0   0   3   0   0   0   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   1   2   0   0   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 1.02839 (all), 1.03209 (group)
Subtype Posterior Probability
03_AB 0.00000169822
04_cpx 0.000000000175234
06_cpx 0.000000182312
07_BC 0.00000455087
08_BC 0.000083143
12_BF 0.0000194985
14_BG 0.000000473635
15_01B 0.0000165848
B 0.999628
K 0.000246123

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 305 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx 07_BC 08_BC 12_BF 14_BG 15_01B   B   K
   03_AB       0      0     0     0     0     0      0   0   0
   04_cpx      1      2     0     0     0     0      0   0   0
   06_cpx      0      7     0     0     0     0      1   1   0
   07_BC       0      1     2     0     0     0      0   0   0
   08_BC       0      0     1     4     0     0      0   0   0
   12_BF       0      1     0     0     7     0      0   2   0
   14_BG       0      0     0     0     0     0      0   0   0
   15_01B      0      0     0     0     0     0      4   1   0
   B           0      0     0     0     1     1      2 260   1
   K           0      0     0     0     0     0      0   3   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