Script to design thousands of primers

Question

[eb13]

Hello,

I am trying to design forward and reverse primers for ~1000 loci for a multiplex PCR reaction. I am targeting the ends of fragments after RE digestion. If I am thinking about this correctly, I imagine to do this I would need a script that would write primers starting at the end of each fragment and add complementary nucleotides sequentially until it reached a desired GC content and melting temp (which would be similar for all primers.) In practice, I am not sure how to do this. Do you know of any software/scripts that will allow this type of high throughput design?

Thank you for your advice and help!

[eb13]

I was not aware of Batch Primer3, thank you for your help!

[lieven.sterck]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 1

[swbarnes2]

You can't make batch primer3 do what you want?

http://batchprimer3.bioinformatics.ucdavis.edu/cgi-bin/batchprimer3/batchprimer3.cgi