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Geno2pheno [coreceptor] 2.5

New September 14th, 2012: The new version introduced in Pfeifer and Lengauer, Bioinformatics, 2012 is now available by selecting
method geno2pheno-C_NGS-Sanger. The method has not been clinically validated yet.
New March 19th, 2012: German guidelines have been updated. New cutoffs are set to 5% and 15%.

On submitting a sequence containing the V3 region of the HIV-1 envelope protein gp120 below, you will obtain a sequence alignment to the reference strain HXB2 and a prediction whether the corresponding virus is capable of using CXCR4 as a coreceptor (R5/X4 or X4 variants) or not (R5 variants).

1. Identifier (optional)
Do not use patient names!
2. Choose Prediction Method:
3. Significance Levels: Please select how conservative the detection of CXCR4 usage should be.

False positive rate is the probability of classifying an R5-virus falsely as X4.   [Help]
Information on the German Treatment Guidelines, the Recommendations from the European Consensus Group
on clinical management of HIV-1 tropism testing
and on how to perform triplicate interpretations can be found here
4. Sequence containing the V3 region of gp120: upload from file (sequences in FASTA format, or single plain or FASTA sequence):

5. Additional parameters
Viral load: Additional markers can help improving the predictions. Please use the nadir (ever lowest level) of
CD4-/CD8-cell counts and CD4 percentages.  [Help]
CD4 percentages:
CD4-cell counts:
CD8-cell counts:
6. Action:

You will make prediction №1167929. Service started June 1, 2004.