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Hi everyone,
I am analyzing intrahost viral quasispecies evolution of Hepatitis C virus by Illumina deep-sequencing from lonigtudinal clinical samples. I aim to determine the type of selection (positive or negative) that is acting on different parts of the viral genome. I am wondering how I should calculate the dN/dS ratio for a viral quasispecies.
Let's say I have a baseline sample A and a sample B from one patient and I would like to analyze the dN/dS ratio for the viral quasispecies between these two samples.
My question is:
1) Do I only consider consensus variants within the viral populations for the calculation of the dN/dS ratio?
2) If not, how do I deal with low frequency variants present within the viral quasispecies when there are multiple SNVs at one position/within a codon?
3) Is there a tool specifically designed to calculate dN/dS ratios from viral quasispecies populations?
4) What model should I use to calculate the dN/dS ratio for Hepatitis C virus? Nei Gojobori ... etc.?
I hope I made myself clear. If something is still unclear, please do not hesitate to ask me.
Thank you very much in advance!
Björn
I am analyzing intrahost viral quasispecies evolution of Hepatitis C virus by Illumina deep-sequencing from lonigtudinal clinical samples. I aim to determine the type of selection (positive or negative) that is acting on different parts of the viral genome. I am wondering how I should calculate the dN/dS ratio for a viral quasispecies.
Let's say I have a baseline sample A and a sample B from one patient and I would like to analyze the dN/dS ratio for the viral quasispecies between these two samples.
My question is:
1) Do I only consider consensus variants within the viral populations for the calculation of the dN/dS ratio?
2) If not, how do I deal with low frequency variants present within the viral quasispecies when there are multiple SNVs at one position/within a codon?
3) Is there a tool specifically designed to calculate dN/dS ratios from viral quasispecies populations?
4) What model should I use to calculate the dN/dS ratio for Hepatitis C virus? Nei Gojobori ... etc.?
I hope I made myself clear. If something is still unclear, please do not hesitate to ask me.
Thank you very much in advance!
Björn
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