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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 66 53 01_AE A Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60079 Z11149 gag 0 207 156 A A A (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.322154 (all), 0.984769 (group)
Subtype Posterior Probability
01_AE 0.53236
A 0.454109
B 0.00677841
C 0.00652811
D 0.000122352
F 0.000000000158323
G 0.0000839068
H 0.00000999388
J 0.00000186791
K 0.00000642547

Cross-Validation of Discriminant Models
Miss-Classification Rate: 206 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    37  29   3   1   1   0   1   0   0
    A        12 111   1   6   1   0   1   0   1
    B         3  10 225  10  12   3   0   1   1
    C        10  31  16 486   0   2   8   0   0
    D         3   3  12   3  55   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: 0.20571 (all), 0.226 (group)
Subtype Posterior Probability
01_AE 0.392
02_AG 0.00000459032
03_AB 0.0000632512
04_cpx 0.0000000160866
06_cpx 0.0000121476
09_cpx 0.0112011
11_cpx 0.0107026
13_cpx 0.000000197904
15_01B 0.00368553
16_A2D 0.000929826
A 0.581401

Cross-Validation of Discriminant Models
Miss-Classification Rate: 89 / 302 at 10 Dimensional MDS
         Predicted
Objective 01_AE 02_AG 03_AB 04_cpx 06_cpx 11_cpx 13_cpx 15_01B 16_A2D   A
   01_AE     36     1     0      0      0      0      0      3      0  32
   02_AG      0    54     0      1      0      0      0      0      0   4
   03_AB      0     0     0      0      0      0      0      0      0   0
   04_cpx     0     0     0      1      2      0      0      0      0   0
   06_cpx     0     0     0      0      7      0      1      0      0   1
   09_cpx     0     0     0      0      0      0      0      0      0   5
   11_cpx     0     0     0      0      0      2      0      0      0   8
   13_cpx     0     0     0      0      3      0      0      0      0   0
   15_01B     4     0     0      0      0      0      0      0      0   1
   16_A2D     0     0     0      0      0      0      0      0      0   2
   A          8     5     1      0      1      2      1      0      2 113

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