Frequently Asked Questions
Question: Did you use Pfam or some other domain prediction software to help in the design of primers?
Answer: No, most domain prediction software uses homology to establish domain signatures. This can give you the conserved region of a domain, but not necessarily the physical boundaries of it. In addition novel domains would be missed since there would be no homology to identify them. For these reasons, we chose to use a systematic approach to our design in which we fragmented proteins in 25-66 amino acid increments using only secondary structure as a guide.