30 bp sequence that does not show hit within a genome
Hi All,
What is the best way to come up with a 30 bp sequence that does not have any hit within the genome? Even better if it does not show hit after allowing 1 or 2 bp mismatches.
Thanks!
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shenwei356
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GR
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I'd make millions of random 30-mers and align it to the given genome with bowtie, with maximum lenient settings. Unmapped sequences will meet your criteria. Pretty much a non-sophisticated sledgehammer method, but easy to do with existing tools and some bash-fu, without reinventing anything.
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