Geno2pheno [hcv]

This is the new service geno2pheno[hcv]. Although we did several test-runs, we cannot guarantee for perfect stability at the moment. In case you observe any problems, please don't hesitate to contact us (sven@mpi-inf.mpg.de)
The list of rules is not complete. Please stay tuned for some updates.

Submit below DNA sequences of the HCV NS3 region or NS5B region or sequences containing both regions.

For NS3 sequences you will obtain a list of mutations according to the NS3 region and predictions of phenotypic resistance of the respective virus to antiviral drugs.
For NS5B sequences you will obtain the genotype and subgenotype using a sequence alignments of the input sequence to HCV consensus sequences.
For sequences containing both regions you will obtain the prediction of the phenotypic resistance of the NS3 region based on the genotype of the NS5B region.

By setting a fold change cutoff you will only obtain mutations with a higher maximal fold change than the threshold. Setting the cutoff '0' all mutations will be obtained. The fold change is based on the IC50 values of the drugs for the different mutations and the wild type.
By changing the "Alignment width" you change the number of nucleotides printed per line in the alignment.
Please note that for reliable predictions the sequences must contain a substantial part of the NS3 or NS5B region.
No clinical decision should be based only on the result of the used algorithm.

1. Identifier (optional)

Do not use patient names!

2. HCV sequence:

upload up a file (plain sequence or FASTA format):

or paste in:

3.Cutoff

fold change cutoff:

4. H77:

Automatically determine the genotype of the input sequence and use the most similar reference sequence for that genotype for the NS3 alignment
Use the H77 strain (genotype 1a) as reference sequence for the NS3 alignment

5. Option:

Alignment width:

6. Action:

You will make prediction №7766. Service started May, 2011.