Primer Design Survey

Angela Merlo angela.merlo at ioez.tu-freiberg.de
Mon Sep 25 08:31:04 EST 2000


Hi Sam,
I do not work very long in primer design and I have search alone and
hard how to do it. I design primers for known homologous protein
sequences.
I think it is a great idea to do a workshop. Where will you do it? in
Ohio? Are you going to open a website or publish the results for the
people who can not visit it? 

Well, I make a comparison of different sources: 
1. web: CODEHOP. blocks of protein sequence and search for posible
degenerated primers. Problem: You do not get a pair of primers and any
other information as Tm, H-bridges...
2. software: DNA star. works very good if you have the whole sequence of
DNA and you look for primers to amplificate it. Problem: It is
complicated (when not imposible) to design primers from a protein
aligment. 
3. myself. problem: headacke. Adventage: if the PCR does not work I am
the only guilty so I do not get angry with computers.

If a mix the three sources I get good primers (sometimes). 

Good luck

Angela






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