How to design oligos based on variable peptide sequence?

Andrea Hansen webmaster at bioinformatik.de
Sat Aug 18 05:11:27 EST 2001


"Emir Khatipov" <khatipo at ZAPuchicago.edu> writes:

Try Codehop:
http://blocks.fhcrc.org/blocks/codehop.html

Andrea

> 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
> 
> 

-- 
Andrea Hansen
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