Question: Script to design thousands of primers
0
gravatar for emb13
16 months ago by
emb130
emb130 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 • 392 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by emb130

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

ADD REPLYlink written 16 months ago by emb130

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 16 months ago by lieven.sterck8.5k
4
gravatar for swbarnes2
16 months ago by
swbarnes28.6k
United States
swbarnes28.6k wrote:

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

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

ADD COMMENTlink written 16 months ago by swbarnes28.6k
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