how to use primer blast for checking primer specificity

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)

4. Then come to No.

- Database Change to “nr”

- Organism Blank or fill specific organism

5. Then click “Get Primers”

Step to use

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