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
gag 0 199 145 B B B (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
938178 CAA42973 gag 0 66 52 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.610869 (all), 0.500743 (group)
Subtype Posterior Probability
01_AE 0.000000000000118521
A 0.00000000315993
B 0.999993
C 0.0000000000507889
D 0.0000009296
F 0.0000000000805147
G 7.39911e-18
H 0.0000000000000684126
J 0.00000590299
K 0.000000000000817028

Cross-Validation of Discriminant Models
Miss-Classification Rate: 23 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    69   3   0   0   0   0   0   0   0   0
    A         0 130   0   0   2   0   1   0   0   0
    B         0   1 261   0   2   1   0   0   0   0
    C         0   1   0 550   0   1   0   1   0   0
    D         0   0   2   0  74   0   0   0   0   0
    F         0   0   0   1   1  13   0   0   0   0
    G         0   0   0   0   0   0  21   0   0   0
    H         0   0   0   0   0   2   0   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.343818 (all), 0.24936 (group)
Subtype Posterior Probability
03_AB 0.0000000000000969096
07_BC 0.000000000000173645
08_BC 0.0000000000000230753
12_BF 0.0000000103704
14_BG 3.56215e-19
15_01B 2.42218e-20
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      3     0     0      0   0
   08_BC      1     4     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     1      0 264

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