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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 0 184 171 C C C (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
71392181 DQ070713 pol 3 554 496 K B Undecided


Detailed result for pol (major) Outlierness: 0.464546 (all), 1.15833 (group)
Subtype Posterior Probability
01_AE 0.000000000245545
A 0.0000000693412
B 0.004047
C 0.994331
D 0.00000914622
F 0.00113158
G 0.000481233
H 0.00000000481675
J 0.0000000000736785
K 0.000000039455

Cross-Validation of Discriminant Models
Miss-Classification Rate: 37 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H
    01_AE    53   3   0   1   0   0   0   0
    A         1  51   2   1   0   0   4   0
    B         0   0 168   0   0   0   0   0
    C         0   0   2 363   0   5   1   0
    D         0   0   1   1  44   0   0   0
    F         0   0   1   0   0   9   2   0
    G         1   1   1   1   0   1  10   1
    H         0   0   1   0   2   0   0   0
    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 pol (nested) Outlierness: 0.726236 (all), 0.731926 (group)
Subtype Posterior Probability
07_BC 0.00142275
08_BC 0.00000148564
10_CD 0.000000288518
C 0.998575

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 376 at 10 Dimensional MDS
         Predicted
Objective 07_BC 10_CD   C
    07_BC     0     0   0
    08_BC     0     0   0
    10_CD     0     3   0
    C         1     2 368

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