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How to use primer-blast for checking primer specificity
Methee Sriprapun, MT, Ph.D.
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Let’s start !
Go to NCBI webpage at: http://www.ncbi.nlm.nih.gov/
Click at “BLAST” (mentioned at red arrow)
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You can see the “BLAST page” Scroll down to “Specialized BLAST” and Click at “Primer-BLAST”
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Two popular functions of Primer-BLAST
1. Designing new primers and specificity checking
- Using sequences from database for primer design
- Following by blast checking specificity of predicted primers
2. Specificity checking of designed primers
- You have your own designed primers
(already had primer sequences)
- Specificity checking of handled primers
THIS PART FOCUS ON SPECIFICITY CHECKING
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Primer-BLAST Tool
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Blast checking use only and
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Step to use
1. You must have your own primer sequences
2. Fill the sequences into
3. You can blank the PCR product size, # of primer
return and Tm of primers (OR use default program)
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4. Then come to No.
- Database Change to “nr”
- Organism Blank or fill specific organism
5. Then click “Get Primers”
Step to use
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Result
Primer information
Matched organism, gene
- Predicted PCR product
- Predicted matched positions between each primer and template
You can scroll down to view additional results