Question: Script to design thousands of primers
0
gravatar for eb13
21 months ago by
eb130
eb130 wrote:

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!

sequence • 452 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by eb130

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

ADD REPLYlink written 21 months ago by eb130

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

ADD REPLYlink written 21 months ago by lieven.sterck10.0k
4
gravatar for swbarnes2
21 months ago by
swbarnes29.6k
United States
swbarnes29.6k wrote:

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

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

ADD COMMENTlink written 21 months ago by swbarnes29.6k
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