how to use primer blast for checking primer specificity
TRANSCRIPT
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
