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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
5rev 21 93 59 ? D 05_DF Undecided
3rev 94 314 176 D D Undecided
env 97 296 90 B B Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60141 CAA41586 rev 0 116 79 B B B (Unambiguous Nested)


Detailed result for 5rev (major) Outlierness: 2.22949 (all), 3.86786 (group)
Subtype Posterior Probability
01_AE 0.00000000822349
A 0.0000107688
B 0.0000150904
C 0.00000035927
D 0.999369
F 0.000605052
G 3.98183e-16
H 0.00000000000105945
J 0.00000000000000491879
K 2.49038e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 58 / 703 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    48   3   0   1   0   0   6   0   0   0
    A         3  47   0   7   0   0   4   0   0   0
    B         0   0 150   2   2   0   0   0   0   0
    C         0   3   0 346   0   1   0   0   0   0
    D         0   1   5   0  39   1   0   0   0   0
    F         0   1   0   2   1   7   0   0   0   1
    G         4   5   0   1   0   0   6   0   0   0
    H         0   1   0   0   0   0   0   2   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   1   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5rev (nested) Outlierness: 5.2932 (all), 12.9019 (group)
Subtype Posterior Probability
05_DF 0.999962
10_CD 4.76084e-18
16_A2D 0.000000000000361198
D 0.000038455

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 53 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD  D
   05_DF      2     0  1
   10_CD      0     2  0
   16_A2D     1     1  0
   D          1     0 45

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3rev (major) Outlierness: 2.59737 (all), 6.07924 (group)
Subtype Posterior Probability
01_AE 0
A 2.52623e-31
B 0.000000257289
C 5.5987e-18
D 1
F 5.38447e-23
G 1.64315e-38
H 0.0000000668614
J 2.76692e-28
K 0.0000000000000139726

Cross-Validation of Discriminant Models
Miss-Classification Rate: 15 / 703 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H
    01_AE    56   0   0   0   0   0   2   0
    A         0  60   0   1   0   0   0   0
    B         0   0 153   0   0   0   0   1
    C         0   1   0 349   0   0   0   0
    D         0   0   0   0  46   0   0   0
    F         0   0   0   4   0   8   0   0
    G         3   0   0   0   0   0  13   0
    H         0   0   0   0   0   0   0   3
    J         0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 3rev (nested) Outlierness: 13.4961 (all), 11.3945 (group)
Subtype Posterior Probability
05_DF 0.0000000134598
10_CD 0.000000101941
16_A2D 0
D 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 53 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      2     0      0  1
   10_CD      0     0      0  2
   16_A2D     0     0      2  0
   D          4     1      0 41

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 2.04166 (all), 2.80457 (group)
Subtype Posterior Probability
01_AE 0.00000000000190681
A 0.000000000612093
B 0.981148
C 0.0000000000000259443
D 0.0188524
F 8.09093e-17
G 0.00000000284593
H 0.00000000571234
J 3.71634e-19
K 0.0000000051781

Cross-Validation of Discriminant Models
Miss-Classification Rate: 75 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H
    01_AE    65   3   0   1   0   0   1   0
    A         0  72   0   8   1   0   1   0
    B         3   2 443   2   0   0   4   0
    C         4  10   0 445   2   1   2   0
    D         0   2   0   1  56   0   0   1
    F         0   0   0   2   1  13   0   0
    G         2   7   2   6   1   0   5   0
    H         1   0   0   0   1   0   0   1
    J         0   0   0   0   0   0   0   0
    K         0   0   0   1   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 2.36687 (all), 2.48027 (group)
Subtype Posterior Probability
03_AB 0.0000000568448
05_DF 0.0000000690077
07_BC 0.000000000000318992
08_BC 0.000000000000579733
10_CD 0.0000533076
12_BF 0.0000000568662
14_BG 0.0218441
15_01B 0.0000000832978
16_A2D 0.0000000448606
B 0.97235
D 0.00575238

Cross-Validation of Discriminant Models
Miss-Classification Rate: 37 / 552 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 12_BF 15_01B 16_A2D   B   D
   03_AB      0     0     0      0      0   0   0
   05_DF      0     0     0      0      0   0   3
   07_BC      0    10     0      0      0   0   0
   08_BC      0     2     0      0      0   0   0
   10_CD      0     0     0      0      0   0   3
   12_BF      0     0     7      0      0   2   1
   14_BG      0     0     0      0      1   0   2
   15_01B     0     0     1      2      0   1   0
   16_A2D     0     1     0      1      0   0   0
   B          2     0     3      7      0 440   2
   D          0     0     1      0      0   3  56

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