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: 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 76 60 B B B (Major agrees Nested with high confidence)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60085 Z11132 gag 2 232 166 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.581475 (all), 0.655381 (group)
Subtype Posterior Probability
01_AE 0.0239023
A 0.00932258
B 0.867536
C 0.0839812
D 0.0133203
F 0.000043928
G 0.0016824
H 0.000081445
J 0.00000195905
K 0.000128405

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  29   3   1   1   0   1   0   0
    A        12 112   1   6   1   0   1   0   0
    B         3   9 225  11  12   3   0   1   1
    C        10  30  16 487   0   2   8   0   0
    D         3   3  10   3  57   0   0   0   0
    F         0   0   1   2   0  10   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: 0.590015 (all), 0.657205 (group)
Subtype Posterior Probability
01_AE 0.0206998
03_AB 0.000000845934
05_DF 0.000000301748
07_BC 0.0000108798
08_BC 0.00000638616
10_CD 0.000000440294
11_cpx 0.0000696111
12_BF 0.000000925548
13_cpx 0.0000263351
14_BG 0.000195037
15_01B 0.0000799364
16_A2D 0.00115332
B 0.830897
C 0.119745
D 0.0271145

Cross-Validation of Discriminant Models
Miss-Classification Rate: 161 / 1013 at 10 Dimensional MDS
         Predicted
Objective 01_AE 05_DF 07_BC 08_BC 10_CD 11_cpx 12_BF 13_cpx 14_BG 15_01B   B
   01_AE     53     0     0     0     0      3     0      0     0      1   2
   03_AB      0     0     0     0     0      0     0      0     0      0   0
   05_DF      0     2     0     0     0      0     0      0     0      0   0
   07_BC      0     0     2     0     0      0     0      0     0      0   0
   08_BC      0     0     1     2     0      0     0      0     0      0   0
   10_CD      0     0     0     0     0      0     0      0     0      0   0
   11_cpx     6     0     0     0     0      0     0      0     0      0   0
   12_BF      0     0     0     0     0      0     8      0     0      0   2
   13_cpx     0     0     0     0     0      0     0      2     0      0   0
   14_BG      0     0     0     0     0      0     0      0     0      0   0
   15_01B     4     0     0     0     0      1     0      0     0      0   0
   16_A2D     0     0     0     0     0      0     0      0     0      0   1
   B          5     1     0     0     1      0     1      0     1      0 230
   C         21     0     3     4     0      2     3      3     0      0  15
   D          4     5     0     0     0      0     0      0     0      0  10
         Predicted
Objective   C   D
   01_AE   12   1
   03_AB    0   0
   05_DF    0   2
   07_BC    1   0
   08_BC    2   0
   10_CD    0   3
   11_cpx   4   0
   12_BF    0   0
   13_cpx   1   0
   14_BG    0   0
   15_01B   0   0
   16_A2D   1   0
   B       17   9
   C      499   3
   D        3  54

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