Geno2pheno[454]: a Web server for the prediction of HIV-1 coreceptor usage from next-generation sequencing data.

Inferring HIV-1 coreceptor usage from a genotype is becoming more and more important for the appropriate treatment of long-term patients. While results are already encouraging where standard bulk-nucleic acid sequencing methods are used, they are limited with respect to the detection of minor variants. In contrast, next-generation sequencing methods (ultradeep sequencing, pyrosequencing) are capable of sequencing virus quasispecies at very low quantities. However, as well as being very expensive, these methods generate vast amounts of data such that sequence analysis has to be automated by computer assistance. Here, we describe the geno2pheno[454] system which handles all processing and prediction steps involved in the prediction of coreceptor usage from massively parallel sequencing data. The system is split into a JAVA preprocessor which is run locally on the client side and a Web server which generates the prediction results. Predictions are based on the same prediction method as used in the geno2pheno[coreceptor] tool.