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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 1020 792 ? J G Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
148925008 ABR19539 pol 0 340 306 G G Undecided


Detailed result for pol (major) Outlierness: 0.869142 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 1.22869e-22
A 0.00000000000000621096
B 5.53113e-29
C 9.25394e-31
D 6.38359e-28
F 1.4525e-24
G 0.0687265
H 0.000110871
J 0.924216
K 0.00694685

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         1  57   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 370   0   0   0   1   0
    D         0   0   0   0  46   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         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: 3.45217 (all), 5.09234 (group)
Subtype Posterior Probability
02_AG 2.07929e-20
04_cpx 0
06_cpx 0.000000000000559409
09_cpx 1.48619e-32
11_cpx 0
13_cpx 0
14_BG 0.000000000123456
G 1
J 4.62428e-44

Cross-Validation of Discriminant Models
Miss-Classification Rate: 3 / 86 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 14_BG  G
   02_AG     43      0      0      0      0      0     0  0
   04_cpx     0      3      0      0      0      0     0  0
   06_cpx     0      0      5      0      0      0     0  0
   09_cpx     0      0      0      4      0      0     0  0
   11_cpx     0      0      0      0     10      0     0  0
   13_cpx     0      0      0      0      0      3     0  0
   14_BG      0      0      0      0      0      0     0  0
   G          0      0      0      0      0      0     1 15
   J          0      0      0      0      0      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