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Free program for primer designing? - Need to check promoter sequence for possible primer binding sites (Apr/03/2007 )


I'm trying to amplify a 5kb promoter sequence and need to design primers for that. I'm wondering if there is a program that can check a given sequence (my template sequence) for possible binding sites of my primers. I'd like to know if my primers might bind somewhere else on the template besides the sequence I want them to bind...



Hi oetziline,

to my knowledge, Primer3 has a mispriming library, at least for human DNA.



The best program to find out whether your primers bind elsewhere in the sequence is a really old Mac program called Amplify, I haven't found anything else that is so simple and easy to use. Of course, unless you have an ancient Mac lying around, you probably won't be able to get your hands on it, so you could see if Primer3 will do it....


.. and it allways helps to BLAST your primer sequences... K.