degenerate oligo design
Tom MacAllister
N490047 at UNIVSCVM.CSD.SCAROLINA.EDU
Mon Dec 6 12:49:03 EST 1993
Dear Netters,
I wish to design a degernate oligo based on peptide sequence for
screening a genomic library. I wondered if anyone could give me an idea as
to the relative importance of number of possible combinations vs number of
known bases. I have the follosing options:
20mer 2048 combinations 14 known bases
17mer 512 combinations 12 known bases
14mer 128 combinations 9 known bases
Is it better to go with more known bases and hope that a lot of the degenerate
combinations will hybridize anyway? My feeling is that the longer oligo would
give me more room to mess with hybridization conditions.
Tom
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