Launch prediction server Query precalculated results
Algorithms Prediction server Database query Output description Benchmark results

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
5tat 0 58 52 B B 12_BF Undecided
vpu 91 324 95 B B B (Major agrees Nested with high confidence)
env 241 2785 1588 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
187947148 ACD41614 env 33 847 551 B B B (Unambiguous Nested)


Detailed result for 5tat (major) Outlierness: 0.570926 (all), 1.47923 (group)
Subtype Posterior Probability
01_AE 9.09147e-11
A 4.6854e-08
B 0.994383
C 6.67608e-11
D 0.000515942
F 4.57039e-07
G 3.38091e-08
H 1.75583e-42
J 3.98133e-09
K 0.00510058

Cross-Validation of Discriminant Models
Miss-Classification Rate: 40 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    42   8   0   0   0   0   2   0   1
    A         3  55   0   1   0   0   4   0   0
    B         0   0 158   1   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0
    D         0   0   3   0  40   1   0   0   0
    F         0   0   0   2   1   8   0   0   1
    G         4   3   0   1   0   0   7   0   0
    H         0   1   0   0   0   0   0   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   1   1   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 1.75931 (all), 5.96181 (group)
Subtype Posterior Probability
03_AB 0.00886191
07_BC 4.20961e-37
08_BC 7.0386e-15
12_BF 0.693739
14_BG 4.20504e-19
15_01B 3.69482e-15
B 0.297399

Cross-Validation of Discriminant Models
Miss-Classification Rate: 18 / 176 at 10 Dimensional MDS
         Predicted
Objective 03_AB 12_BF 14_BG 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      0     0     0      0   0
   08_BC      0     0     0      0   0
   12_BF      0     4     0      0   6
   14_BG      0     0     1      1   0
   15_01B     0     0     0      2   0
   B          1     7     0      0 151

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.787834 (all), 0.95069 (group)
Subtype Posterior Probability
01_AE 1.09358e-16
A 3.7302e-14
B 1
C 3.91097e-13
D 2.02822e-07
F 5.90743e-10
G 1.47791e-13
H 3.41501e-12
J 4.23313e-21
K 4.1084e-20

Cross-Validation of Discriminant Models
Miss-Classification Rate: 13 / 932 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    44   2   0   0   0   0   0   0   0
    A         3  64   1   0   0   0   0   2   0
    B         0   0 321   0   0   0   0   0   0
    C         0   0   0 397   0   0   0   0   0
    D         0   0   0   0  54   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  22   0   0
    H         0   3   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   2
    K         0   0   0   0   0   1   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (nested) Outlierness: 1.12515 (all), 1.10797 (group)
Subtype Posterior Probability
03_AB 5.94747e-06
08_BC 8.46972e-23
12_BF 0.0591079
14_BG 1.61144e-28
15_01B 1.07064e-16
B 0.940886

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 340 at 10 Dimensional MDS
         Predicted
Objective 12_BF 14_BG 15_01B   B
   03_AB      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     0      0  12
   14_BG      0     3      0   0
   15_01B     0     0      2   0
   B          1     0      0 320

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 0.994928 (all), 1.00898 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 0
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   0   0   0   0   0   0   0   0
    A         0  82   0   0   0   0   0   0   0
    B         0   0 454   0   0   0   0   0   0
    C         0   0   0 464   0   0   0   0   0
    D         0   0   0   0  60   0   0   0   0
    F         0   0   0   0   0  15   0   0   1
    G         0   0   0   0   0   0  23   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 env (nested) Outlierness: 1.01034 (all), 1.00973 (group)
Subtype Posterior Probability
03_AB 0.00144539
07_BC 0
08_BC 0
12_BF 1.1466e-32
14_BG 0.00110189
15_01B 5.81016e-16
B 0.997453

Cross-Validation of Discriminant Models
Miss-Classification Rate: 17 / 484 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      8     2     0     0      0   0
   08_BC      2     0     0     0      0   0
   12_BF      0     0     8     0      0   2
   14_BG      0     0     0     3      0   0
   15_01B     0     0     0     0      4   0
   B          0     0     0     0     10 444

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