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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 0 270 204 J J Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
10944817 CAC14034 pol 0 90 70 J 11_cpx Undecided


Detailed result for pol (major) Outlierness: 2.87603 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 9.72821e-18
A 4.36502e-18
B 1.90104e-23
C 4.71072e-17
D 2.05407e-17
F 0.0000168086
G 1.7613e-26
H 2.22738e-22
J 0.999983
K 0.00000000000204239

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 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         6  52   0   0   0   0   1   0   0   0
    B         0   0 160   0   5   3   0   0   0   0
    C         0   0   0 370   0   0   0   0   1   0
    D         0   3   0   0  43   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   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 4.14693 (all), 3.4e38 (group)
Subtype Posterior Probability
06_cpx 0
11_cpx 0.000000465207
13_cpx 0.00000000000000125963
J 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 1 / 19 at 10 Dimensional MDS
         Predicted
Objective 06_cpx 11_cpx 13_cpx
   06_cpx      5      0      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