peptide library - (Aug/11/2014 )

I want to start making a peptide library for a virus. I have the capsid sequence. How do I now proceed and how do I chose the peptides?

Perhaps if you give us a bit more info on what you're doing. Like what application will this be used for and what assay you're planning to run. In general most people use linear peptides that are about 15 aa in length and then use a sliding window of 3-4 aa, i.e. overlap of 11-12 aa (depending on your budget) and scan the entire protein. These days there are however more complicated ways of going about it, like cyclically constrained peptides and the like but as I said it depends on your desired application.