Searching a genome to find primer sequences that do not occur

Dr. Duncan Clark Duncan at
Tue Feb 27 06:17:10 EST 2001

In article <3A9B7F29.21F3A49D at>, the eminent Simon Andrews at
BBSRC Biotechnology and Biological Sciences Research Council wrote
>This means you
>could start out searching (for example) 5-mers. If none of those were
>unique then search 6-mers.  Repeat until something isn't found. 

8-mers would be a good bet as you could use a unique one at the 3'end of
a primer without worrying 'too much' about the remainder of the primer. 

Go further and eliminate all 8-mers outside the range 40-60% GC. 

Eliminate all runs of A's, T's G's and C's at the 3' end of say more
than 2 and anything of greater than or equal to 4 anywhere. 

Deliberately pick a GC, CC, GG, or CG pair at the 3' end.

Eliminate hairpins - bit more tricky to program although just
eliminating internal palindromes of greater than 4 may be enough.

Now that must make it a bit more realistic and narrow it all down.

Being an old fashioned programmer I can see my True Basic re-appearing
for the first time in years.  

The problem with being on the cutting edge is that you occasionally get 
sliced from time to time....

Duncan Clark
GeneSys Ltd.
Tel: +44(0)1252376288
FAX: +44(0)8701640382

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