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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