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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
pol 0 297 231 J 13_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
125745481 ABN55131 pol 0 99 79 H 04_cpx Undecided


Detailed result for pol (major) Outlierness: 1.1673 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.0000000000000877491
A 0.00000000731654
B 0.0000000486808
C 0.000000000000162368
D 0.00000648075
F 0.00000160149
G 0.00000244148
H 0.000642184
J 0.99931
K 0.0000376625

Cross-Validation of Discriminant Models
Miss-Classification Rate: 22 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    57   0   0   0   0   0   0   0   0   0
    A         5  54   0   0   0   0   0   0   0   0
    B         0   0 161   0   4   3   0   0   0   0
    C         0   0   0 370   0   0   0   0   0   1
    D         0   3   1   0  42   0   0   0   0   0
    F         0   0   0   0   1  11   0   0   0   0
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   0   0   0   1   2   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   1   0   0   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 1.07863 (all), 2.30062 (group)
Subtype Posterior Probability
06_cpx 3.71678e-29
11_cpx 0
13_cpx 1
J 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 2 / 19 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      4      1      0
   11_cpx      0     10      0
   13_cpx      0      0      3
   J           0      0      0

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