Geno2pheno [coreceptor] 2.5

	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.
	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:	original g2p coreceptor geno2pheno-C_NGS-Sanger
3. Significance Levels:	Please select how conservative the detection of CXCR4 usage should be. – please select – German Treatment Guidelines Recommendations from the European Consensus Group on clinical management of HIV-1 tropism testing (10% FPR) Optimized cutoffs based on analysis of clinical data from MOTIVATE (2% and 5.75% FPR) false positive rate (1 - specificity) = 1% false positive rate (1 - specificity) = 2.5% false positive rate (1 - specificity) = 5% false positive rate (1 - specificity) = 10% false positive rate (1 - specificity) = 15% false positive rate (1 - specificity) = 20% 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): or paste in:
5. Additional parameters	Viral load: not determined < 100 100-1000 1000-10000 10000-100000 > 100000 Additional markers can help improving the predictions. Please use the nadir (ever lowest level) of CD4-/CD8-cell counts and CD4 percentages.  [Help] CCR5-genotype: not determined WT/WT WT/d32 d32/d32 CD4 percentages: not determined < 5 5-10 10-15 15-20 20-25 25-30 30-35 35-40 40-45 45-50 50-55 55-60 60-65 65-70 70-75 75-80 80-85 85-90 90-95 ≥ 95 CD4-cell counts: not determined < 25 26-50 51-100 101-150 151-200 201-250 251-300 301-351 351-400 401-450 451-500 501-600 601-700 701-800 801-900 901-1000 > 1000 CD8-cell counts: not determined < 100 101-200 201-300 301-400 401-500 501-600 601-700 701-800 801-900 901-1000 1001-1100 1101-1200 1201-1300 1301-1400 1401-1500 > 1500
6. Action:	Align and Predict Reset (Clear Session) Load sample sequences Switch to vertical layout

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You will make prediction №546010. Service started June 1, 2004.