I'm very new to molecular biology and I'm helping start up a lab. My supervisor is also new to molecular biology and we are learning as we go so please excuse me if I sound ignorant.
I have a few questions about degenerate primers.
1.) Is there an advantage of using the AA sequence over Nucleotide sequences when aligning sequences for degenerate primer design?
2.) When aligning sequences do we pick the most highly conserved area and design the primers around that area?
3.) Is Vector NTI a good program for this? I have also heard of using ClustralW??
4.) Degenerated Primers are generally the same price as regular primers? Where is a good place to purchase the primers if I'm on the East Coast of Canada.
Any tips or advice would be greatly appreciated as I am very new to this area of research.