How to design oligos based on variable peptide sequence?

David Micklem dmicklem at cmgm.nospam.invalid
Tue Aug 14 16:20:29 EST 2001


In article <WDce7.333$65.25282 at news.uchicago.edu>, Emir Khatipov
<khatipo at ZAPuchicago.edu> wrote:

>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
>


Well, it shouldn't be too tough to work that out for yourself! Five
minutes with the New England Biolabs catalogue gives:

Ala GCN
Arg CGN or AGR (but MGR will inclide Ser too!)
Asn AAY
Asp GAY
Cys TGY
Gln CAR
Glu GAR
Gly GGN
His CAY
Ile ATH
Leu CTN or TTR (but YTN will include Phe too!)
Lys AAR
Met ATG
Phe TTY
Pro CCN
Ser TCN or AGY (but YSN will include all sorts of stuff)
Thr ACN
Trp TGG
Tyr TAY
Val GTN

although you might want to double check it!

David

-- 
D.R. Micklem,              Time flies like an arrow... 
Dept. of Anatomy,          Fruit flies like a banana.
Cambridge University,      Email:dmicklem at cmgm.stanford.edu 
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