I am working on designing dsRNA and I want to check each smaller section of the sequence for possible off-target effects.
I have a 500 bp sequence. I want to write a script that extracts all possible 20 bp fragments within the longer sequence. I am interested in automating this rather than doing it manually because I may repeat the process several times.
Then I want to BLAST each one of those 20 bp sequences against the honey bee genome (with the GOI masked) to make sure each fragment doesn't have perfect alignment anywhere other than the GOI.
Any help is very appreciated!