Searching a genome to find primer sequences that do not occur

Richard P. Grant rpg14 at yahoo.co.uk.invalid
Tue Feb 27 09:38:23 EST 2001


In article <IsxsekACXjm6EACG at genesys.demon.co.uk>, "Dr. Duncan Clark" 
<Duncan at genesys.demon.co.uk> wrote:

> 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.

I'm not a computer biologist, so don't know if this would work in a 
finite time frame . . .  but  how about starting by scanning the genome 
with a window of 15 nt that moves by one nt each time, such that you get 
(genome length - 14) 15 mers?

Ideally you then compare that data set with all possible 15 mers ! (4 to 
the fifteenth?  That's just over a billion.  Hmm might be doable)

But you could array the 15 mers vertically and do some kind of pattern 
elimination search so that you take the first oligo, change 1 or 2 nt, 
search the array for a match, and reiterate until you don't get a match?  
I thought of maybe some position-specific thing but can't quite see how 
that would work.

-- 
Richard P. Grant                                     MRC Lab of Mol Biol
rpg 'at' mrc-lmb.cam.ac.uk   http://www2.mrc-lmb.cam.ac.uk/personal/rpg/
 -- I laugh in the face of danger. Then I hide until it passes --


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