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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
5tat 0 144 124 K 16_A2D Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
37693970 AAP33768 tat 0 87 79 A A A (Major agrees Nested with high confidence)


Detailed result for 5tat (major) Outlierness: 3.68199 (all), 15.1511 (group)
Subtype Posterior Probability
01_AE 0.0000000125817
A 0.0143021
B 1.32539e-23
C 0.000000000153496
D 2.02632e-17
F 6.66888e-31
G 0.000000000000765525
H 0.000917556
J 0.000251821
K 0.984528

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 659 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    51   0   0   0   0   0   2   0   0   0
    A         6  52   1   1   0   1   1   0   0   1
    B         0   0 159   0   0   0   0   0   0   0
    C         0   0   0 307   0   0   0   0   0   0
    D         0   0   1   0  43   0   0   0   0   0
    F         0   0   0   0   2   9   0   1   0   0
    G         0   0   0   0   0   0  15   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   1   0   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 5.16031 (all), 22.1211 (group)
Subtype Posterior Probability
02_AG 0.0000000000000274581
03_AB 2.66883e-24
04_cpx 0.00000000000150887
06_cpx 4.83841e-21
09_cpx 0.0000000016791
11_cpx 3.54852e-16
13_cpx 2.10708e-39
16_A2D 0.999888
A 0.00011195
K 3.14702e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 128 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A  K
   02_AG     35     0      0      0      0      0      0      0  0  0
   03_AB      0     0      0      0      0      0      0      0  0  0
   04_cpx     0     0      0      0      0      0      0      0  3  0
   06_cpx     0     0      0      6      0      0      0      0  0  0
   09_cpx     0     0      0      0      3      0      0      0  1  0
   11_cpx     0     0      0      0      0      8      0      0  0  1
   13_cpx     0     0      0      0      0      0      3      0  0  0
   16_A2D     0     0      0      0      0      0      0      2  0  0
   A          0     1      2      0      0      0      0      2 58  0
   K          0     0      0      1      0      0      0      0  0  1

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