How to design oligos based on variable peptide sequence?

Bryan Maloney bjm10 at cornell.edu
Tue Aug 14 07:41:53 EST 2001


"Emir Khatipov" <khatipo at ZAPuchicago.edu> wrote in
news:AVUd7.261$65.19645 at news.uchicago.edu: 

> Dear netters,
> I want to construct a peptide library. I have a 10 peptide stretch in
> which some aa residues have to be conserved, others should vary,
> basically something like:
> 
> A-(V,I,L,M, or C)-K-(F, Y, or W)-P-(S, T, G, or D)-...etc.
> 
> Could you share your experience on how I should better design
> degenerate oligonucleotide sequence based on peptide sequences like

It may sound crude (indeed, it is crude), but I'd use a spreadsheet rather 
than track down a piece of specialized software.  By the time I find the 
software and learn to use it, I'll have the spreadsheet work finished.



-- 
"Cape Cod Salsa--somehow that's just not right."




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