HOW to design a single strand primer

Question

[kumajis]

I want to design a primer only for a single strand (forward or reverse but not both) because the target is a fusion gene and not sure what fusion sequence is.

For most primer design tools is set for two primer design (like primer blast or primer3 which conside compartblity for both primer), is there some method for just design one primer and consider specificity on the whole genome.

Answer 1

[i.sudbery]

Its possible to tell primer3 to design only one primer. Just below the sequence input box there are tick boxes for "Pick left primer", "Pick hybridization probe", "pick right primer". By default both "Pick left primer" and "Pick right primer" are selected, but you can unselect one if you only want to design one primer.

You will then need to manually check the primer for uniqueness by blasting it or blatting it yourself.