How to use primer-blast for

checking primer specificity

Methee Sriprapun, MT, Ph.D.
 Let’s start !
 Go to NCBI webpage at: http://www.ncbi.nlm.nih.gov/
 Click at “BLAST” (mentioned at red arrow)
 You can see the “BLAST page”  Scroll down to
“Specialized BLAST” and Click at “Primer-BLAST”
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

Primer-BLAST Tool

 






 

 Blast checking  use only  and 

 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)
 Step to use 
 4. Then come to No. 
- Database  Change to “nr”
- Organism  Blank or fill specific organism

5. Then click “Get Primers”

 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

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