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Please give examples, question somewhat unclear.
Hi, ATpoint.
For example, if I want to design a unique 9 bp sequence for artificial zinc finger protein that does not recognize host cell's upstream 2000 bp sequence sets, I think I should screen all 4^9 sequence sets and count how many matches occur in the given upstream 2000 bp sequence sets. Is there any tool that I can use to figure out the number of occurrence of multiple sequence pairs or figure out the unique 9 bp sequence?
you can try using unique kmer identifying tools given a fasta file. Based on the length of your genome, you can calculate maximum possible kmer. Feed the genome to software that identifies kmer sizes of your choice.
Thank you cpad0112.
For asking more information, can you recommend me a good tool to figure out unique and not existing K-mer? Because What I mean by "unique" is not "occuring one time", but "no identical sequences exist in the given genome".