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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
rev 0 116 79 ? B B B (Unambiguous Nested)


Subtype Prediction for Associated Nucleotide Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60140 X58781 3rev 94 314 176 D D Undecided
5rev 21 93 59 D 05_DF Undecided
env 97 296 90 B B Undecided


Detailed result for rev (major) Outlierness: 0.534545 (all), 0.956466 (group)
Subtype Posterior Probability
01_AE 0.000000000000339746
A 0.000000000108846
B 0.994697
C 0.00000000819968
D 0.00530338
F 0.000000000181299
G 0.0000000185043
H 0.0000000000159035
J 0.00000000000832642
K 0.00000000329951

Cross-Validation of Discriminant Models
Miss-Classification Rate: 32 / 703 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J
    01_AE    54   0   0   1   0   0   3   0   0
    A         0  57   0   3   0   0   0   0   1
    B         0   0 152   0   1   0   1   0   0
    C         0   2   0 343   0   2   3   0   0
    D         0   0   1   0  45   0   0   0   0
    F         0   0   0   3   0   9   0   0   0
    G         1   0   0   5   0   0  10   0   0
    H         0   0   0   1   0   0   1   1   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   1   0   0   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for rev (nested) Outlierness: 0.653896 (all), 0.955617 (group)
Subtype Posterior Probability
03_AB 0.000952392
07_BC 4.01071e-16
08_BC 0.00000000000432863
12_BF 0.000460866
14_BG 0.0000000402412
15_01B 0.0000000000179177
B 0.998587

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 173 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0     0      0   0
   07_BC      0     0     0     0      0   0
   08_BC      0     2     0     0      0   0
   12_BF      0     0     0     8      0   1
   14_BG      0     0     1     0      1   0
   15_01B     0     0     0     0      4   0
   B          1     0     0     0      0 153

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