Primer for Unkown Protein PCR - How to design primer for unknown protein (May/18/2010 )

Good day!
I'm a noob in molecular biology. Please, jelp me guys

I want to design primer to identify (only) Heat-resistant Mold (HRM) in sample. But i cant find any specific proteins in HRM, because no such data in NCBI.

1. Can I design primer without knowing specific target protein?
2. Can I design primer by comparing the genome of the HRMs and find a region that similiar in all species of HRM? Is it reliable? And what tool to use?
3. Many journals use ITS regions for detection, but i think it will give positive result for all fungi. Am I right?

common HRMs: Byssochlamys fulva, Byssochlamys nivea, Neosartorya fischeri, Talaromyces macrosporus, Talaromyces flavus
maybe someone have made primers for these HRMs before

Many thanks in advance

Xylph on May 19 2010, 12:05 AM said:

i want to make primer to detect contamination of these molds (Byssochlamys fulva, Byssochlamys nivea, Neosartorya fischeri, Talaromyces macrosporus, Talaromyces flavus) in the sample. so i need specific gene / domain which is specific on those species. They arent in the same genus, but they have something in common. All of them are heat resistant (~95C), so i think they will have specific domains on their coding sequence for the heat adaptation.

same principle: use ctx gene primer to detect Vibrio cholerae in sample.

Thx for the reply
=D