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Primer specificity

Primer specificity - DNA Forum

Primer specificity - Discuss DNA, the molecule of hereditary. Topics include DNA structure, DNA replication, DNA function.


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Old 07-09-2011, 05:15 AM
Pipette Filler
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Default Primer specificity



Dear All,

Hello!

I searched for an 18S rRNA gene of an organism on the NCBI website. I found the sequence and designed primers using the primer tool on the same website. Now, I want to check the primer specificity (i.e. can I use this primer as an identification tool to detect a specific species using PCR) and the question is:
do I need to BLAST the primer sequence (both forward and reverse) or to BLAST the sequence of the amplified fragment (PCR product). Many thanks in advance.

Best regards,

Mohammad
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Old 07-21-2011, 07:21 PM
Pipette Filler
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Default Re: Primer specificity

Check your primers using in silico PCR: [Only registered users see links. ]

blasting the primer sequences is never bad..
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