I was hoping someone out there can give me some advice on assembling PCR products which have been amplified using degenerate primers (primers containing ambiguous nucleotides e.g. TAYGGNCCNACNGA). I would like to mask the degenerate primer sequences, as I do not want sequences to be aligned on these regions. As a workaround I thought that I could generate a list of all permutations of my 2 pairs of primers, and pass these to either vector_clip or cross_match - but I end up with over 20,000 permutations! I don't want to grind our system to a halt... is there a simple way to do this in Staden?

Thanks in advance,