How to design oligos based on variable peptide sequence?

Emir Khatipov khatipo at ZAPuchicago.edu
Mon Aug 13 13:25:15 EST 2001


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 above. I am sort of
stumbled by the fact that I have to check all the combinations of codons for
variable aminoacid residues, which seems to be just a kind of work I will
mess up real easily. There must be some well established way of doing such a
thing, or a software, or web tool...

I would greatly appreciate any help.
Thank you.
Emir Khatipov
University of Chicago





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