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Primer3 vs Primer BLAST


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#1 kristian

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Posted 15 November 2009 - 06:05 AM

I am designing primers for gene expression studies based on a known sequence. I am using Primer3 and Primer BLAST. I know that Primer BLAST uses Primer 3 but the two still give me two different different sets of primer suggestions. Primer 3 gives a better set of primers with regards to secondary structure formation, but PrimerBLAST must be giving more specific pairs since it already check the primers using BLAST.
I checked if the two suggested similar primer pairs but found none.
Maybe you can share which software are you more confident of using. Thanks!

Edited by kristian, 15 November 2009 - 06:08 AM.


#2 biobio

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Posted 15 November 2009 - 08:01 AM

I am designing primers for gene expression studies based on a known sequence. I am using Primer3 and Primer BLAST. I know that Primer BLAST uses Primer 3 but the two still give me two different different sets of primer suggestions. Primer 3 gives a better set of primers with regards to secondary structure formation, but PrimerBLAST must be giving more specific pairs since it already check the primers using BLAST.
I checked if the two suggested similar primer pairs but found none.
Maybe you can share which software are you more confident of using. Thanks!


In my opinion they are both good - the option to design primers that span intron-exon junctions in Primer BLAST is also very useful.

These days I use PrimerBLAST, but I subject the primers to my own BLAST search and criteria just to be sure :)

In the case of most genes you can have an extended list of good primers so I wouldn't worry too much about it!

#3 Mighty Mouse

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Posted 15 November 2009 - 10:15 AM

I've used both programs, and I have to say I like Primer3 a bit better just because it gives additional information about the secondary structure of the primers and reduces the amount of time for obtaining good primers. I always check the primers using Net Primer, but PrimerBLAST drives me nuts because they don't rank the primers at all. I'm not sure I understand why they don't, since it's basically built off of Primer3, so presumably the information should be there. Anyway, that's my two cents.
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#4 Helios

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Posted 16 November 2009 - 01:26 AM

i use pimer3 to design primers and check the specificity with again with primer BLAST.it works fine for me. personally i prefer Primer3 sofware...




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