Question: Script to design thousands of primers
0
gravatar for emb13
6 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 • 255 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by emb130

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

ADD REPLYlink written 6 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 6 months ago by lieven.sterck6.3k
4
gravatar for swbarnes2
6 months ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

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

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

ADD COMMENTlink written 6 months ago by swbarnes27.0k
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