Using Primer--BLAST from NCBI for checking primers

1. How to use primer-blast for checking primer specificity
Methee Sriprapun, MT, Ph.D.

2. Let’s start !
Go to NCBI webpage at: http://www.ncbi.nlm.nih.gov/
Click at “BLAST” (mentioned at red arrow)

3. You can see the “BLAST page”  Scroll down to “Specialized BLAST” and Click at “Primer-BLAST”

4. 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

5. Primer-BLAST Tool
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6. Blast checking  use only  and 
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7. 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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8. 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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9. 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

10. THANK YOU FOR YOUR ATTENTION
Sriprapun.m@gmail.com