Searching a genome to find primer sequences that do not occur

Roland Hubner rhubner at gins.uia.ac.be
Mon Mar 5 12:22:30 EST 2001


> Is there any way to search a small genome to find primer sequences that
> do not exist in that genome e.g. say anything from 15-22mers.

Hi Duncan,

 I know of 2 primer design programs that select most specific primers 
according to the rarety of the 3'-nona/octamer sequence... Thusly, that
has certainly been done before (even when complete genome not 
available)... 

 I am pretty sure that this was based on paper out in NAR years back... 
(sorry, PubMed connection down right now here... title has very likely 
word "octamer" in it)

Roland






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