Designing unique DNA sequence set

Question

[chansik]

Hi, I'm trying to find a unique sequence with certain length (from 9 to 20 bp) that are not exist in given large size of DNA sequence.

Is there any useful tool to identify unique short sequences?

Thank you

[ATpoint]

Please give examples, question somewhat unclear.

[chansik]

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?

[cpad0112]

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.

[chansik]

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".