1. Our program can be mainly used to design siRNAs/shRNAs against mRNAs of vertebrates, however, some trials against fly mRNAs
also had pretty good knockdowns.
2. It can also probabably be used to design siRNAs against 5' and 3' UTRs and non-coding RNAs.
1). Choose the database you want to blast.
Choose mismatch cutoff, more mismatches will give you less off-target problems. You can try higher cutoff value first,
if nothing is available, choose lower cutoff values.
Click submit. The ranks are based on some experimental evidences that a couple of positions have some preferences.