How to design oligos based on variable peptide sequence?

Emir Khatipov khatipo at ZAPuchicago.edu
Tue Aug 14 11:51:44 EST 2001


If I will really have to go for spreadsheet-assisted design of oligos, I
would appreciate if someone could send me or post here a table of genetic
code based on degenerate nucleotide code (M for C or A, R for A or G, etc).
Don't remember seeing such a thing anywhere.
Thanks
Emir

"Emir Khatipov" <khatipo at ZAPuchicago.edu> wrote in message
news:2uce7.331$65.25051 at news.uchicago.edu...
> OK, Brian,
> I think you response is a bit out of point. I clearly asked for software.
I
> certainly understand that spreadsheet can do that, but it is a harder and
> longer way. Time is really an issue for me right now, so I am looking for
> quicker solution.
> Emir
>
> "Bryan Maloney" <bjm10 at cornell.edu> wrote in message
> news:9lb6ah$kqp$4 at news01.cit.cornell.edu...
> > "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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