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
pol 0 197 184 B F Undecided


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
71392197 DQ070721 pol 0 592 537 K F Undecided


Detailed result for pol (major) Outlierness: 0.684138 (all), 1.23086 (group)
Subtype Posterior Probability
01_AE 0.00251629
A 0.00692889
B 0.533011
C 0.00773325
D 0.000000262989
F 0.397951
G 0.0514072
H 0.0000015426
J 0.00000000000948659
K 0.000450752

Cross-Validation of Discriminant Models
Miss-Classification Rate: 32 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    54   3   0   0   0   0   0   0   0
    A         1  52   1   1   0   0   4   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   1 365   1   2   2   0   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0   8   3   0   1
    G         1   2   1   0   0   1  10   1   0
    H         0   1   1   0   1   0   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.874072 (all), 1.52253 (group)
Subtype Posterior Probability
02_AG 0.00127581
03_AB 0.00000000218845
04_cpx 0.0000000125729
05_DF 0.000000000336216
06_cpx 0.00412259
07_BC 0.000000007003
08_BC 0.000000471544
09_cpx 0.0000862742
11_cpx 0.0139546
12_BF 0.0000808069
13_cpx 0.0000669378
14_BG 0.00000147957
15_01B 0.00347686
B 0.0337682
F 0.897791
G 0.0453746

Cross-Validation of Discriminant Models
Miss-Classification Rate: 56 / 283 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 05_DF 06_cpx 08_BC 09_cpx 11_cpx 12_BF 13_cpx
   02_AG     34     0      1     0      0     0      3      0     0      2
   03_AB      0     0      0     0      0     0      0      0     0      0
   04_cpx     0     0      2     0      0     0      0      0     0      0
   05_DF      0     0      0     2      0     0      0      0     0      0
   06_cpx     0     0      0     0      0     0      1      0     0      0
   07_BC      0     0      0     0      0     0      0      0     0      0
   08_BC      0     0      0     0      0     0      0      0     0      0
   09_cpx     1     0      0     0      1     0      1      0     0      0
   11_cpx     0     0      0     0      0     0      0      8     0      0
   12_BF      0     0      0     0      0     0      0      0     0      0
   13_cpx     0     0      0     0      0     0      0      1     0      2
   14_BG      0     0      0     0      0     0      0      0     0      0
   15_01B     1     0      0     0      0     0      0      1     0      0
   B          0     0      0     0      0     1      0      1     4      0
   F          2     0      1     0      0     0      1      0     0      0
   G          1     1      0     0      1     0      0      1     0      1
         Predicted
Objective 14_BG 15_01B   B   F   G
   02_AG      0      0   0   2   1
   03_AB      0      0   0   0   0
   04_cpx     0      0   0   1   0
   05_DF      0      0   1   0   0
   06_cpx     1      0   0   0   3
   07_BC      0      0   0   0   0
   08_BC      0      0   0   0   0
   09_cpx     0      0   0   1   0
   11_cpx     0      1   1   0   0
   12_BF      0      0   9   0   0
   13_cpx     0      0   0   0   0
   14_BG      0      0   0   0   0
   15_01B     0      0   0   0   1
   B          0      0 162   0   0
   F          0      0   0   6   2
   G          1      0   0   0  10

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