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Wednesday, May 1, 2013

A Simple Method to find PCR Product length from Primer Sequence


This post describes how to find the ampicon / PCR Product size from primer sequence.

1. Go to NCBI Nucleotide Blast, in the "Enter accession number(s), gi(s), or FASTA sequence(s) box"

Type your forward primer sequence followed by four "n" and your reverse primer sequence.

Lets say  your Forward Primer sequence is :

Forward Primer: GGAATGTTATTGCTAACAC [Enter your Forward Primer Sequence]
Reverse Primer: CACCATTAAGTACATCAC [Enter your Reverse Primer Sequence]

In the FASTA sequence box Enter the primer sequence in this format:

"GGAATGTTATTGCTAACACnnnnCACCATTAAGTACATCAC"
"your Foward primer sequencennnnyour Reverse primer sequence"

pcr product length

Press on BLAST and wait for the result screen to come.

You will get the BLAST Result Screen like the one below.



Scroll down to see the matching sequences of your given query.

 Click on the First link (the one with highest matching % from the list).



By substracting the lower sequence number value of the forward strand from the lower sequence number value of the reverse strand you can find out the PCR product length.

In this case,

2003 - 1581 = 422bp

BLAST your Primer Sequence..!!!

Reference for Primer sequence
http://jcm.asm.org/content/37/5/1269.full