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Primer for Unkown Protein PCR


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#1 Xylph

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Posted 18 May 2010 - 08:05 AM

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

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 :lol:

#2 paramitay

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Posted 21 May 2010 - 01:02 AM

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


confusing here..
1. what species are u using now?
2. what u means with 'identify (only) Heat-resistant Mold (HRM) in sample'? does it means, u want to know what kind of species (HRM) contain in ur samples?

#3 Xylph

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Posted 21 May 2010 - 02:01 AM

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




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