Searching a genome to find primer sequences that do not occur

Dr. Duncan Clark Duncan at nospam.demon.co.uk
Thu Mar 1 04:42:35 EST 2001


In article <97h8nd$2k526$1 at reader02.wxs.nl>, the eminent Gys de Jongh at
Planet Internet wrote
>nice idea
>how about these next moves ?
>take the list of (genome lenght -14) 15 mers
>calculate the base-4 number of each 15 mer :
>if  A=0 C=1 G=2 T=3 (others will do also) than .......A A G T C C T
>= ...0*(4^6) + 0*(4^5) + 2*(4^4) + 3*(4^3) + 1*(4^2) + 1*(4^1) + 3*(4^0)
>sort the list of (genome lenght -14) 15 mers and their base-4 numbers
>in ascending base-4 number.
>Now each place where the sequence is interrupted
>will be the start of a not present 15-mer primer.
>In this way you don't need a list of all possible 15-mers
>or a comparison of the (genome length - 14) 15 mers
>with this list.

That's a neat idea.

Thanks

Duncan
-- 
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
http://www.dnamp.com
http://www.genesys.demon.co.uk








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