kristian, on Nov 15 2009, 07:05 AM, said:
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!